******************************************************************************** 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 cds-WP_011947911.1 1.0000 100 dnaX 1.0000 100 cds-WP_003359494.1 1.0000 100 cds-WP_003404855.1 1.0000 100 cds-WP_011947938.1 1.0000 100 cds-WP_011947952.1 1.0000 100 cds-WP_003356351.1 1.0000 100 rho 1.0000 100 rpmE 1.0000 100 cds-WP_011947984.1 1.0000 100 cds-WP_003356899.1 1.0000 100 atpE 1.0000 100 cds-WP_003355885.1 1.0000 100 cds-WP_011947988.1 1.0000 100 atpA 1.0000 100 atpG 1.0000 100 atpD 1.0000 100 cds-WP_003387838.1 1.0000 100 cds-WP_011947999.1 1.0000 100 cds-WP_003355819.1 1.0000 100 rpoN 1.0000 100 cds-WP_003399034.1 1.0000 100 cds-WP_003390961.1 1.0000 100 cds-WP_011948050.1 1.0000 100 cds-WP_011948062.1 1.0000 100 cds-WP_011948063.1 1.0000 100 cds-WP_011948072.1 1.0000 100 cds-WP_003355791.1 1.0000 100 cds-WP_011948077.1 1.0000 100 cds-WP_003362768.1 1.0000 100 cds-WP_011948118.1 1.0000 100 cds-WP_003362795.1 1.0000 100 cds-WP_011948172.1 1.0000 100 cds-WP_011948175.1 1.0000 100 cds-WP_003355838.1 1.0000 100 cds-CBO_RS18635 1.0000 100 cds-WP_011948219.1 1.0000 100 cds-WP_003359683.1 1.0000 100 cds-WP_011948232.1 1.0000 100 cds-WP_003359806.1 1.0000 100 cds-WP_011986143.1 1.0000 100 cds-WP_003403434.1 1.0000 100 cds-WP_011948324.1 1.0000 100 cds-WP_011948327.1 1.0000 100 cds-WP_011948333.1 1.0000 100 cds-WP_011948348.1 1.0000 100 cds-WP_003356776.1 1.0000 100 cds-WP_011948365.1 1.0000 100 cds-WP_011948369.1 1.0000 100 cds-WP_011948372.1 1.0000 100 cds-WP_011948378.1 1.0000 100 greA 1.0000 100 cds-WP_230869867.1 1.0000 100 cds-WP_225900976.1 1.0000 100 cds-WP_011948438.1 1.0000 100 cds-WP_011948452.1 1.0000 100 cds-WP_011948453.1 1.0000 100 cds-WP_011948466.1 1.0000 100 cds-WP_003387694.1 1.0000 100 cds-WP_011948471.1 1.0000 100 cds-WP_011948534.1 1.0000 100 cds-WP_011948541.1 1.0000 100 cds-WP_011948545.1 1.0000 100 cds-WP_011948547.1 1.0000 100 cds-WP_003399301.1 1.0000 100 cds-WP_003357080.1 1.0000 100 cds-WP_011948557.1 1.0000 100 cds-WP_011948563.1 1.0000 100 cds-WP_011948567.1 1.0000 100 cds-WP_011948570.1 1.0000 100 cds-WP_079995886.1 1.0000 100 cds-WP_011948597.1 1.0000 100 cds-WP_011948600.1 1.0000 100 cds-WP_011948616.1 1.0000 100 cds-WP_011948628.1 1.0000 100 cds-WP_011948668.1 1.0000 100 cds-WP_011948696.1 1.0000 100 cds-WP_003356907.1 1.0000 100 cds-WP_011948703.1 1.0000 100 cds-WP_003356424.1 1.0000 100 cds-WP_011948759.1 1.0000 100 cds-WP_011948763.1 1.0000 100 cds-WP_011948772.1 1.0000 100 rpsA 1.0000 100 cds-WP_003356138.1 1.0000 100 cds-WP_011948833.1 1.0000 100 cds-WP_011948840.1 1.0000 100 cds-WP_011948844.1 1.0000 100 cds-WP_003356834.1 1.0000 100 cds-WP_011948871.1 1.0000 100 mtnA 1.0000 100 cds-WP_011948894.1 1.0000 100 cds-WP_003358748.1 1.0000 100 cds-WP_003358712.1 1.0000 100 cds-WP_011948948.1 1.0000 100 ychF 1.0000 100 cds-WP_003393623.1 1.0000 100 cds-WP_003358553.1 1.0000 100 cds-WP_011949080.1 1.0000 100 cds-WP_003388928.1 1.0000 100 cds-WP_011949087.1 1.0000 100 cds-WP_011949091.1 1.0000 100 cds-CBO_RS07675 1.0000 100 cds-WP_011949098.1 1.0000 100 cds-WP_011949106.1 1.0000 100 cds-WP_011949120.1 1.0000 100 cds-WP_011949137.1 1.0000 100 cds-WP_011949138.1 1.0000 100 cds-WP_011986272.1 1.0000 100 cds-WP_011949150.1 1.0000 100 cds-WP_011949159.1 1.0000 100 cds-WP_011986282.1 1.0000 100 cds-WP_011986286.1 1.0000 100 cds-CBO_RS08185 1.0000 100 cds-WP_164928177.1 1.0000 100 cds-WP_012047595.1 1.0000 100 cds-WP_003395988.1 1.0000 100 cds-WP_011986310.1 1.0000 100 cds-WP_011986315.1 1.0000 100 lexA 1.0000 100 cds-WP_003392901.1 1.0000 100 cds-WP_012047676.1 1.0000 100 cds-WP_003358959.1 1.0000 100 scpB 1.0000 100 nusB 1.0000 100 efp 1.0000 100 cds-WP_003358480.1 1.0000 100 cds-WP_011986476.1 1.0000 100 cds-WP_011986487.1 1.0000 100 cds-WP_011986494.1 1.0000 100 cds-WP_011986498.1 1.0000 100 cds-WP_003385301.1 1.0000 100 treR 1.0000 100 cds-WP_012047704.1 1.0000 100 cds-WP_003358481.1 1.0000 100 cds-WP_011986542.1 1.0000 100 cds-WP_011986544.1 1.0000 100 cds-WP_011986554.1 1.0000 100 cds-WP_011986562.1 1.0000 100 cds-WP_003358306.1 1.0000 100 cds-WP_003384878.1 1.0000 100 cds-WP_011986616.1 1.0000 100 cds-WP_003402124.1 1.0000 100 cds-WP_003358234.1 1.0000 100 cds-WP_011986653.1 1.0000 100 cds-WP_011986682.1 1.0000 100 cds-WP_011986684.1 1.0000 100 cds-WP_012047750.1 1.0000 100 cds-WP_012047752.1 1.0000 100 cds-WP_003391706.1 1.0000 100 cds-WP_003358274.1 1.0000 100 cds-WP_011986719.1 1.0000 100 cds-WP_011986731.1 1.0000 100 cds-WP_011986754.1 1.0000 100 cds-WP_011986758.1 1.0000 100 cds-WP_011986765.1 1.0000 100 cds-WP_003395350.1 1.0000 100 cds-WP_011986767.1 1.0000 100 cds-WP_011986769.1 1.0000 100 cds-WP_156226176.1 1.0000 100 cds-WP_012047775.1 1.0000 100 cds-WP_041350636.1 1.0000 100 cds-WP_341349816.1 1.0000 100 cds-WP_012047848.1 1.0000 100 cds-WP_012047850.1 1.0000 100 rpsO 1.0000 100 infB 1.0000 100 cds-WP_004440225.1 1.0000 100 cds-WP_003388362.1 1.0000 100 nusA 1.0000 100 cds-WP_011986794.1 1.0000 100 tsf 1.0000 100 rpsB 1.0000 100 codY 1.0000 100 rplS 1.0000 100 rpsP 1.0000 100 rpmF 1.0000 100 prdR 1.0000 100 rpmB 1.0000 100 rpoZ 1.0000 100 cds-WP_257262151.1 1.0000 100 nrdR 1.0000 100 sigG 1.0000 100 sigE 1.0000 100 sigK 1.0000 100 cds-WP_003391911.1 1.0000 100 cds-WP_011986902.1 1.0000 100 cds-WP_011986903.1 1.0000 100 cds-WP_011986937.1 1.0000 100 cds-WP_003404508.1 1.0000 100 cds-WP_011986984.1 1.0000 100 rfbF 1.0000 100 cds-WP_011987038.1 1.0000 100 cds-WP_011987040.1 1.0000 100 cds-WP_011987070.1 1.0000 100 cds-WP_011987090.1 1.0000 100 cds-WP_011987095.1 1.0000 100 cds-WP_011987106.1 1.0000 100 cds-WP_011987107.1 1.0000 100 cds-WP_012047951.1 1.0000 100 cds-WP_012047976.1 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 selB 1.0000 100 cds-WP_003357849.1 1.0000 100 cds-WP_012048020.1 1.0000 100 rpmA 1.0000 100 cds-WP_012048022.1 1.0000 100 rplU 1.0000 100 polA 1.0000 100 cds-WP_012099500.1 1.0000 100 cds-WP_012048067.1 1.0000 100 cds-WP_012048092.1 1.0000 100 sigF 1.0000 100 cds-WP_012048124.1 1.0000 100 rplT 1.0000 100 rpmI 1.0000 100 infC 1.0000 100 cds-WP_003357340.1 1.0000 100 cds-WP_012048183.1 1.0000 100 cds-WP_003357370.1 1.0000 100 cds-WP_012048201.1 1.0000 100 cds-WP_012048232.1 1.0000 100 cds-WP_012048290.1 1.0000 100 cds-WP_012048304.1 1.0000 100 cds-WP_003360267.1 1.0000 100 rpsD 1.0000 100 cds-WP_012048331.1 1.0000 100 cds-WP_012048343.1 1.0000 100 rpsI 1.0000 100 rplM 1.0000 100 rplQ 1.0000 100 cds-WP_003357472.1 1.0000 100 rpsD_2 1.0000 100 rpsK 1.0000 100 rpsM 1.0000 100 rpmJ 1.0000 100 infA 1.0000 100 cds-WP_003357464.1 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_003357636.1 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 tuf 1.0000 100 fusA 1.0000 100 rpsG 1.0000 100 rpsL 1.0000 100 cds-WP_012048355.1 1.0000 100 rpoC 1.0000 100 rpoB 1.0000 100 rplL 1.0000 100 rplJ 1.0000 100 rplA 1.0000 100 rplK 1.0000 100 nusG 1.0000 100 rpmG 1.0000 100 tuf_2 1.0000 100 sigH 1.0000 100 cds-WP_003357349.1 1.0000 100 fusA_2 1.0000 100 greA_2 1.0000 100 cds-WP_003359441.1 1.0000 100 cds-WP_003359471.1 1.0000 100 mfd 1.0000 100 cds-WP_012048397.1 1.0000 100 cds-WP_003400977.1 1.0000 100 cds-WP_003359449.1 1.0000 100 cds-WP_003359341.1 1.0000 100 cds-WP_012048431.1 1.0000 100 rplI 1.0000 100 rpsR 1.0000 100 rpsF 1.0000 100 cds-WP_012048450.1 1.0000 100 noc 1.0000 100 rpmH 1.0000 100 cds-WP_011949166.1 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 -maxw 50 -maxsites 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= 50 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= 29800 N= 298 sample: seed= 0 hsfrac= 0 searchsize= 29800 norand= no csites= 1000 Letter frequencies in dataset: A 0.355 C 0.138 G 0.113 T 0.393 Background letter frequencies (from file dataset with add-one prior applied): A 0.355 C 0.138 G 0.113 T 0.393 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF TCCTCCMY MEME-1 width = 8 sites = 50 llr = 527 E-value = 4.6e-055 ******************************************************************************** -------------------------------------------------------------------------------- Motif TCCTCCMY MEME-1 Description -------------------------------------------------------------------------------- Simplified A ::::::5: pos.-specific C 1aa:aa34 probability G :::::::: matrix T 9::a::26 bits 3.1 2.8 ** ** 2.5 ** ** 2.2 ** ** Relative 1.9 ** ** Entropy 1.6 ** ** (15.2 bits) 1.3 ***** 0.9 ****** * 0.6 ****** * 0.3 ******** 0.0 -------- Multilevel TCCTCCAT consensus CC sequence T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TCCTCCMY MEME-1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- rpmJ 87 1.07e-06 GGTTTATTAT TCCTCCCC AATAAC rpmH 85 3.81e-06 TCTAGAGTTT TCCTCCAC GACACTTT rpmG 87 3.81e-06 CAATACATGA TCCTCCAC ATCTAG rplK 87 3.81e-06 TTGGTGTATA TCCTCCAC ATTTTA rplJ 85 3.81e-06 CATTTGACAC TCCTCCAC CTGTGTGT rpsL 88 3.81e-06 GATTAATACT TCCTCCAC GTGCA rplC 86 3.81e-06 ATTATACAAC TCCTCCAC GTTTCTT rplW 85 3.81e-06 AGGTTTTAAC TCCTCCAC ATACGTAT rplX 85 3.81e-06 ATTATTATGT TCCTCCAC CGATTTAT rplF 87 3.81e-06 TAACCTCTTA TCCTCCAC GTTATT rplO 86 3.81e-06 CGTATCATTC TCCTCCAC ATTAATA rpsM 84 3.81e-06 CATCCATAAG TCCTCCAC ATTTGAAAT rpsD_2 84 3.81e-06 TATATCATTA TCCTCCAC ATTTTAAAT rplU 87 3.81e-06 CTGACCTTAC TCCTCCAC AAAAAT cds-WP_011986902.1 86 3.81e-06 AGATAAAAGT TCCTCCAC ATTACCA rpmF 87 3.81e-06 GATGAGTCAT TCCTCCAC AAATGT rpsP 87 3.81e-06 TCTAAAAATT TCCTCCAC TTTTTG cds-WP_341349816.1 71 3.81e-06 TTACTGTTGT TCCTCCAC TAATATATAC rpsR 88 6.85e-06 AAATTTCTCT TCCTCCCT ATCAA nusG 66 6.85e-06 TCACTTATTT TCCTCCCT TTATCCCTAT rpsG 87 6.85e-06 GAATTACAAT TCCTCCCT TCTTTT rpsJ 86 6.85e-06 CATGGTCTTT TCCTCCCT TGTAATT rplB 88 6.85e-06 TTCGATTTCT TCCTCCCT TTGTT rpsC 88 6.85e-06 CAAATTCTTC TCCTCCCT TAAGC cds-WP_003357636.1 88 6.85e-06 AGCAATTAAT TCCTCCCT TTAGA rpsE 88 6.85e-06 AAAATTTTTT TCCTCCCT TTATT rpsK 88 6.85e-06 TTTATTCCAT TCCTCCCT TTTCG sigE 88 6.85e-06 CCTTAATATA TCCTCCCT GAAAA rplS 86 6.85e-06 TTTTTTAATT TCCTCCCT TACGTGT cds-WP_003395350.1 87 6.85e-06 AATTAATTAG TCCTCCCT TTTTCT rplV 86 1.47e-05 TATTCGACCT TCCTCCAT TTTAAGT rplE 87 1.47e-05 TTAAGAACTT TCCTCCAT ATTTCC rpmD 86 1.47e-05 TAAAATCCAA TCCTCCAT TGACCGG rplQ 85 1.47e-05 CAAATTCCAT TCCTCCAT ATCCTCTC cds-WP_003360267.1 86 1.47e-05 ATCGGAATAA TCCTCCAT AATAAAA rplT 86 1.47e-05 TCCTCGTGTT TCCTCCAT CAAACCC cds-WP_003359471.1 83 1.81e-05 AATAAATAAT TCCTCCTC AGAATAATTA sigK 87 1.81e-05 TTCGTGATAA TCCTCCTC GTCGAA rplM 88 2.01e-05 TTTTATCAAT CCCTCCCT TTTAC rpsU 87 2.01e-05 TTGATCGCCT CCCTCCCT CTTTTG rfbF 87 2.01e-05 ATAATTTTGC CCCTCCCT TTATTT tuf_2 87 2.88e-05 TCGTATTTTT TCCTCCTT TATTTT tuf 87 2.88e-05 TTGTGTTTTT TCCTCCTT TATTTT rpsD 90 2.88e-05 TATATCATAA TCCTCCTT CTT prmA 87 2.88e-05 AGAATAAAAT TCCTCCTT AAAAAG rpoZ 86 2.88e-05 AATCGTAGTT TCCTCCTT AAATAAG tsf 87 2.88e-05 ATCAATTTTA TCCTCCTT ATATAT cds-WP_011986794.1 89 2.88e-05 GTAATGAGAA TCCTCCTT ATTA cds-WP_011948452.1 86 2.88e-05 TAATAAAACA TCCTCCTT TCTATAA rpsQ 87 3.15e-05 ATTTTGACTT CCCTCCAT TTAGGA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TCCTCCMY MEME-1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- rpmJ 1.1e-06 86_[+1]_6 rpmH 3.8e-06 84_[+1]_8 rpmG 3.8e-06 86_[+1]_6 rplK 3.8e-06 86_[+1]_6 rplJ 3.8e-06 84_[+1]_8 rpsL 3.8e-06 87_[+1]_5 rplC 3.8e-06 85_[+1]_7 rplW 3.8e-06 84_[+1]_8 rplX 3.8e-06 84_[+1]_8 rplF 3.8e-06 86_[+1]_6 rplO 3.8e-06 85_[+1]_7 rpsM 3.8e-06 83_[+1]_9 rpsD_2 3.8e-06 83_[+1]_9 rplU 3.8e-06 86_[+1]_6 cds-WP_011986902.1 3.8e-06 85_[+1]_7 rpmF 3.8e-06 86_[+1]_6 rpsP 3.8e-06 86_[+1]_6 cds-WP_341349816.1 3.8e-06 70_[+1]_22 rpsR 6.8e-06 87_[+1]_5 nusG 6.8e-06 65_[+1]_27 rpsG 6.8e-06 86_[+1]_6 rpsJ 6.8e-06 85_[+1]_7 rplB 6.8e-06 87_[+1]_5 rpsC 6.8e-06 87_[+1]_5 cds-WP_003357636.1 6.8e-06 87_[+1]_5 rpsE 6.8e-06 87_[+1]_5 rpsK 6.8e-06 87_[+1]_5 sigE 6.8e-06 87_[+1]_5 rplS 6.8e-06 85_[+1]_7 cds-WP_003395350.1 6.8e-06 86_[+1]_6 rplV 1.5e-05 85_[+1]_7 rplE 1.5e-05 86_[+1]_6 rpmD 1.5e-05 85_[+1]_7 rplQ 1.5e-05 84_[+1]_8 cds-WP_003360267.1 1.5e-05 85_[+1]_7 rplT 1.5e-05 85_[+1]_7 cds-WP_003359471.1 1.8e-05 82_[+1]_10 sigK 1.8e-05 86_[+1]_6 rplM 2e-05 87_[+1]_5 rpsU 2e-05 86_[+1]_6 rfbF 2e-05 86_[+1]_6 tuf_2 2.9e-05 86_[+1]_6 tuf 2.9e-05 86_[+1]_6 rpsD 2.9e-05 89_[+1]_3 prmA 2.9e-05 86_[+1]_6 rpoZ 2.9e-05 85_[+1]_7 tsf 2.9e-05 86_[+1]_6 cds-WP_011986794.1 2.9e-05 88_[+1]_4 cds-WP_011948452.1 2.9e-05 85_[+1]_7 rpsQ 3.2e-05 86_[+1]_6 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TCCTCCMY MEME-1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF TCCTCCMY width=8 seqs=50 rpmJ ( 87) TCCTCCCC 1 rpmH ( 85) TCCTCCAC 1 rpmG ( 87) TCCTCCAC 1 rplK ( 87) TCCTCCAC 1 rplJ ( 85) TCCTCCAC 1 rpsL ( 88) TCCTCCAC 1 rplC ( 86) TCCTCCAC 1 rplW ( 85) TCCTCCAC 1 rplX ( 85) TCCTCCAC 1 rplF ( 87) TCCTCCAC 1 rplO ( 86) TCCTCCAC 1 rpsM ( 84) TCCTCCAC 1 rpsD_2 ( 84) TCCTCCAC 1 rplU ( 87) TCCTCCAC 1 cds-WP_011986902.1 ( 86) TCCTCCAC 1 rpmF ( 87) TCCTCCAC 1 rpsP ( 87) TCCTCCAC 1 cds-WP_341349816.1 ( 71) TCCTCCAC 1 rpsR ( 88) TCCTCCCT 1 nusG ( 66) TCCTCCCT 1 rpsG ( 87) TCCTCCCT 1 rpsJ ( 86) TCCTCCCT 1 rplB ( 88) TCCTCCCT 1 rpsC ( 88) TCCTCCCT 1 cds-WP_003357636.1 ( 88) TCCTCCCT 1 rpsE ( 88) TCCTCCCT 1 rpsK ( 88) TCCTCCCT 1 sigE ( 88) TCCTCCCT 1 rplS ( 86) TCCTCCCT 1 cds-WP_003395350.1 ( 87) TCCTCCCT 1 rplV ( 86) TCCTCCAT 1 rplE ( 87) TCCTCCAT 1 rpmD ( 86) TCCTCCAT 1 rplQ ( 85) TCCTCCAT 1 cds-WP_003360267.1 ( 86) TCCTCCAT 1 rplT ( 86) TCCTCCAT 1 cds-WP_003359471.1 ( 83) TCCTCCTC 1 sigK ( 87) TCCTCCTC 1 rplM ( 88) CCCTCCCT 1 rpsU ( 87) CCCTCCCT 1 rfbF ( 87) CCCTCCCT 1 tuf_2 ( 87) TCCTCCTT 1 tuf ( 87) TCCTCCTT 1 rpsD ( 90) TCCTCCTT 1 prmA ( 87) TCCTCCTT 1 rpoZ ( 86) TCCTCCTT 1 tsf ( 87) TCCTCCTT 1 cds-WP_011986794.1 ( 89) TCCTCCTT 1 cds-WP_011948452.1 ( 86) TCCTCCTT 1 rpsQ ( 87) CCCTCCAT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TCCTCCMY MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 27714 bayes= 10.2462 E= 4.6e-055 -1229 -79 -1229 123 -1229 286 -1229 -1229 -1229 286 -1229 -1229 -1229 -1229 -1229 135 -1229 286 -1229 -1229 -1229 286 -1229 -1229 43 121 -1229 -98 -1229 153 -1229 61 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TCCTCCMY MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 50 E= 4.6e-055 0.000000 0.080000 0.000000 0.920000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.480000 0.320000 0.000000 0.200000 0.000000 0.400000 0.000000 0.600000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TCCTCCMY MEME-1 regular expression -------------------------------------------------------------------------------- TCCTCC[ACT][TC] -------------------------------------------------------------------------------- Time 32.46 secs. ******************************************************************************** ******************************************************************************** MOTIF GGAGGW MEME-2 width = 6 sites = 47 llr = 453 E-value = 1.6e-036 ******************************************************************************** -------------------------------------------------------------------------------- Motif GGAGGW MEME-2 Description -------------------------------------------------------------------------------- Simplified A ::9::5 pos.-specific C :::::1 probability G aa1aa2 matrix T :::::3 bits 3.1 ** ** 2.8 ** ** 2.5 ** ** 2.2 ** ** Relative 1.9 ** ** Entropy 1.6 ** ** (13.9 bits) 1.3 ***** 0.9 ***** 0.6 ***** 0.3 ***** 0.0 ------ Multilevel GGAGGA consensus T sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGAGGW MEME-2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------ cds-WP_003392901.1 87 6.54e-06 TTATATTTTT GGAGGG ATTTGCTA cds-WP_011948871.1 88 6.54e-06 CATGATATAA GGAGGG GGTAATA cds-WP_079995886.1 88 6.54e-06 CAATAGTCAA GGAGGG GATTTAT cds-WP_011948563.1 89 6.54e-06 ATGATTTCAA GGAGGG ATATTA cds-WP_011948466.1 89 6.54e-06 TATCTATATA GGAGGG AGATTA cds-WP_011948372.1 90 6.54e-06 GTGGGTATAA GGAGGG GTTAT cds-WP_011948175.1 86 6.54e-06 ATGTGAAATG GGAGGG GATAATAAT cds-WP_003404855.1 89 6.54e-06 TTTAATTTTA GGAGGG ATACAT cds-WP_011987107.1 89 2.71e-05 TATATATTTC GGAGGA ATTGTA cds-WP_011986719.1 87 2.71e-05 AATTAAAATC GGAGGA AATTTGAT cds-WP_003358480.1 90 2.71e-05 AATTAACTAA GGAGGA TAAAA cds-WP_011949091.1 90 2.71e-05 TATTTTATAT GGAGGA TAATC cds-WP_011949080.1 90 2.71e-05 TTTTCTATTA GGAGGA ATAGC mtnA 89 2.71e-05 AAAGTAAAGA GGAGGA TTAAAA cds-WP_011948833.1 91 2.71e-05 ATTTTTTGGA GGAGGA TATA cds-WP_011948763.1 87 2.71e-05 TAAATTTAAT GGAGGA GTACAAGA cds-WP_011948759.1 91 2.71e-05 TGTGAGTATA GGAGGA CTTT cds-WP_011948668.1 91 2.71e-05 ATGTATAATT GGAGGA ATTT cds-WP_011948628.1 88 2.71e-05 GAAACTTTTA GGAGGA ATATATG cds-WP_011948570.1 83 2.71e-05 TAATAAAGAT GGAGGA TATTTACAAA cds-WP_011948534.1 88 2.71e-05 TATCTTGCTT GGAGGA TTACTAT cds-WP_003387694.1 90 2.71e-05 ATACAAGAAA GGAGGA TAATA cds-WP_011948438.1 89 2.71e-05 TTTATTTAAT GGAGGA AACAAA cds-WP_230869867.1 37 2.71e-05 TTTGTCAATA GGAGGA TGCCGTTGTT greA 85 2.71e-05 CATATCTTGG GGAGGA TTATTTGTAC cds-WP_011948219.1 90 2.71e-05 TGAGCTTTTG GGAGGA ATTTT cds-WP_011948118.1 86 2.71e-05 ATTATGTTAG GGAGGA TTAATATCA atpE 88 2.71e-05 TTAAATTTAA GGAGGA ATTTGGT cds-WP_003359449.1 89 4.98e-05 TATCAATTTG GGAGGT AACTAA cds-WP_003400977.1 88 4.98e-05 TAAATACAAT GGAGGT AATTATA rpmB 87 4.98e-05 ACAATTTTAG GGAGGT GTTTTTAA cds-WP_012047848.1 88 4.98e-05 ATAATATATA GGAGGT AGTCAAT cds-WP_011948597.1 88 4.98e-05 AATTAGATAA GGAGGT GAAGAAA cds-WP_011948557.1 80 4.98e-05 ATCTAGTATA GGAGGT ATACTAAATT cds-WP_011948547.1 88 4.98e-05 AAAAATATTC GGAGGT AAAAATA cds-WP_011948378.1 91 4.98e-05 TTGCTTTTGG GGAGGT TTTT cds-WP_003403434.1 89 4.98e-05 GTAGAACTTT GGAGGT GAAGTT cds-WP_011947999.1 91 4.98e-05 TTTAATATTT GGAGGT AAAG atpD 90 4.98e-05 CTCAAAGGTA GGAGGT GTACT atpG 90 4.98e-05 TATCTCTGAA GGAGGT AAAAT rpoN 80 5.19e-05 AAAATCAAAG GGGGGG TAGGAATTTA cds-WP_011948077.1 89 5.99e-05 AATAATTTAT GGAGGC AATGGA cds-WP_003355885.1 86 5.99e-05 AAGGCCGAAG GGAGGC TTCCTATAT dnaN 88 5.99e-05 TGTTAATAAA GGAGGC TAATTTT cds-WP_003395988.1 25 6.64e-05 GTGAAAACAA GGGGGA TTACACATGG cds-WP_011948369.1 89 6.64e-05 GTCAACTATA GGGGGA GTATAT rpsT 89 7.37e-05 AAAAACACGA GGGGGT GAAAAA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGAGGW MEME-2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- cds-WP_003392901.1 6.5e-06 86_[+2]_8 cds-WP_011948871.1 6.5e-06 87_[+2]_7 cds-WP_079995886.1 6.5e-06 87_[+2]_7 cds-WP_011948563.1 6.5e-06 88_[+2]_6 cds-WP_011948466.1 6.5e-06 88_[+2]_6 cds-WP_011948372.1 6.5e-06 89_[+2]_5 cds-WP_011948175.1 6.5e-06 85_[+2]_9 cds-WP_003404855.1 6.5e-06 88_[+2]_6 cds-WP_011987107.1 2.7e-05 88_[+2]_6 cds-WP_011986719.1 2.7e-05 86_[+2]_8 cds-WP_003358480.1 2.7e-05 89_[+2]_5 cds-WP_011949091.1 2.7e-05 89_[+2]_5 cds-WP_011949080.1 2.7e-05 89_[+2]_5 mtnA 2.7e-05 88_[+2]_6 cds-WP_011948833.1 2.7e-05 90_[+2]_4 cds-WP_011948763.1 2.7e-05 86_[+2]_8 cds-WP_011948759.1 2.7e-05 90_[+2]_4 cds-WP_011948668.1 2.7e-05 90_[+2]_4 cds-WP_011948628.1 2.7e-05 87_[+2]_7 cds-WP_011948570.1 2.7e-05 82_[+2]_12 cds-WP_011948534.1 2.7e-05 87_[+2]_7 cds-WP_003387694.1 2.7e-05 89_[+2]_5 cds-WP_011948438.1 2.7e-05 88_[+2]_6 cds-WP_230869867.1 2.7e-05 36_[+2]_58 greA 2.7e-05 84_[+2]_10 cds-WP_011948219.1 2.7e-05 89_[+2]_5 cds-WP_011948118.1 2.7e-05 85_[+2]_9 atpE 2.7e-05 87_[+2]_7 cds-WP_003359449.1 5e-05 88_[+2]_6 cds-WP_003400977.1 5e-05 87_[+2]_7 rpmB 5e-05 86_[+2]_8 cds-WP_012047848.1 5e-05 87_[+2]_7 cds-WP_011948597.1 5e-05 87_[+2]_7 cds-WP_011948557.1 5e-05 79_[+2]_15 cds-WP_011948547.1 5e-05 87_[+2]_7 cds-WP_011948378.1 5e-05 90_[+2]_4 cds-WP_003403434.1 5e-05 88_[+2]_6 cds-WP_011947999.1 5e-05 90_[+2]_4 atpD 5e-05 89_[+2]_5 atpG 5e-05 89_[+2]_5 rpoN 5.2e-05 79_[+2]_15 cds-WP_011948077.1 6e-05 88_[+2]_6 cds-WP_003355885.1 6e-05 85_[+2]_9 dnaN 6e-05 87_[+2]_7 cds-WP_003395988.1 6.6e-05 24_[+2]_70 cds-WP_011948369.1 6.6e-05 88_[+2]_6 rpsT 7.4e-05 88_[+2]_6 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGAGGW MEME-2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF GGAGGW width=6 seqs=47 cds-WP_003392901.1 ( 87) GGAGGG 1 cds-WP_011948871.1 ( 88) GGAGGG 1 cds-WP_079995886.1 ( 88) GGAGGG 1 cds-WP_011948563.1 ( 89) GGAGGG 1 cds-WP_011948466.1 ( 89) GGAGGG 1 cds-WP_011948372.1 ( 90) GGAGGG 1 cds-WP_011948175.1 ( 86) GGAGGG 1 cds-WP_003404855.1 ( 89) GGAGGG 1 cds-WP_011987107.1 ( 89) GGAGGA 1 cds-WP_011986719.1 ( 87) GGAGGA 1 cds-WP_003358480.1 ( 90) GGAGGA 1 cds-WP_011949091.1 ( 90) GGAGGA 1 cds-WP_011949080.1 ( 90) GGAGGA 1 mtnA ( 89) GGAGGA 1 cds-WP_011948833.1 ( 91) GGAGGA 1 cds-WP_011948763.1 ( 87) GGAGGA 1 cds-WP_011948759.1 ( 91) GGAGGA 1 cds-WP_011948668.1 ( 91) GGAGGA 1 cds-WP_011948628.1 ( 88) GGAGGA 1 cds-WP_011948570.1 ( 83) GGAGGA 1 cds-WP_011948534.1 ( 88) GGAGGA 1 cds-WP_003387694.1 ( 90) GGAGGA 1 cds-WP_011948438.1 ( 89) GGAGGA 1 cds-WP_230869867.1 ( 37) GGAGGA 1 greA ( 85) GGAGGA 1 cds-WP_011948219.1 ( 90) GGAGGA 1 cds-WP_011948118.1 ( 86) GGAGGA 1 atpE ( 88) GGAGGA 1 cds-WP_003359449.1 ( 89) GGAGGT 1 cds-WP_003400977.1 ( 88) GGAGGT 1 rpmB ( 87) GGAGGT 1 cds-WP_012047848.1 ( 88) GGAGGT 1 cds-WP_011948597.1 ( 88) GGAGGT 1 cds-WP_011948557.1 ( 80) GGAGGT 1 cds-WP_011948547.1 ( 88) GGAGGT 1 cds-WP_011948378.1 ( 91) GGAGGT 1 cds-WP_003403434.1 ( 89) GGAGGT 1 cds-WP_011947999.1 ( 91) GGAGGT 1 atpD ( 90) GGAGGT 1 atpG ( 90) GGAGGT 1 rpoN ( 80) GGGGGG 1 cds-WP_011948077.1 ( 89) GGAGGC 1 cds-WP_003355885.1 ( 86) GGAGGC 1 dnaN ( 88) GGAGGC 1 cds-WP_003395988.1 ( 25) GGGGGA 1 cds-WP_011948369.1 ( 89) GGGGGA 1 rpsT ( 89) GGGGGT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGAGGW MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 6 n= 28310 bayes= 11.329 E= 1.6e-036 -1220 -1220 314 -1220 -1220 -1220 314 -1220 136 -1220 -41 -1220 -1220 -1220 314 -1220 -1220 -1220 314 -1220 40 -111 76 -51 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGAGGW MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 6 nsites= 47 E= 1.6e-036 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.914894 0.000000 0.085106 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.468085 0.063830 0.191489 0.276596 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGAGGW MEME-2 regular expression -------------------------------------------------------------------------------- GGAGG[AT] -------------------------------------------------------------------------------- Time 65.13 secs. ******************************************************************************** ******************************************************************************** MOTIF YTYYCCTCCT MEME-3 width = 10 sites = 47 llr = 454 E-value = 3.9e-028 ******************************************************************************** -------------------------------------------------------------------------------- Motif YTYYCCTCCT MEME-3 Description -------------------------------------------------------------------------------- Simplified A 231::::2:: pos.-specific C 4135aa38a1 probability G :::::::::1 matrix T 4655::71:8 bits 3.1 2.8 ** * 2.5 ** * 2.2 ** * Relative 1.9 ** * Entropy 1.6 ** ** (13.9 bits) 1.3 *** ** 0.9 ****** 0.6 * ******* 0.3 ********** 0.0 ---------- Multilevel CTTCCCTCCT consensus TACT C sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif YTYYCCTCCT MEME-3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------- rpmI 84 7.82e-08 CGCATTATTG CTCCCCTCCT TTAGTGT cds-WP_011986542.1 22 7.82e-08 TCTTTTGTTT CTCCCCTCCT CAATGCAATT rpoC 84 3.28e-07 TGTAATTAAA CTTCCCTCCT ATATGGG rpsI 85 3.28e-07 TAACGTCCGA CTTCCCTCCT ATTTTT rpsF 81 4.21e-07 GGCAATCAGG CACCCCTCCT CCACTTATAT rpsS 84 1.25e-06 TACTAACACG CTTCCCTCCG TTTATAT fusA 84 2.37e-06 TTAAACTTTG CTACCCTCCT TTTCGTT rplD 85 2.37e-06 TTAAATTTAT CTTTCCTCCT ACGTCT cds-WP_003357370.1 84 2.37e-06 AAACATTACC CTACCCTCCT TAAAATA cds-WP_011986937.1 22 2.37e-06 TCAAAATACT TCCCCCTCCT TTTGGTAAAT cds-WP_012048290.1 87 3.49e-06 TTCACCATTA ATCCCCCCCT CTAT cds-WP_003358234.1 83 3.49e-06 AATTGTAAAA TTTCCCCCCT TTAGTTTA rplP 84 4.36e-06 ATTGCGTATT CCTTCCTCCT TATTGTA sigH 87 5.51e-06 TATAAATAAA ACCCCCCCCT ATGG cds-WP_003357849.1 84 5.51e-06 TTATCTTTAA TTCTCCTCCT AATAAAA cds-WP_003385301.1 22 5.51e-06 CTCTATTTAT TTCTCCCCCT CTATTTATTT rpsH 84 7.10e-06 AAGCTTTTCG CTTTCCTCCG TTTTATT rpoD 81 7.10e-06 TTTATTACCG CTTTCCTCCG ATGTGAATAT rplN 83 8.56e-06 CGTTTTTCGG CTTTCCTCCC ATAAAATG cds-WP_011948365.1 85 8.99e-06 TCTTTTTTAA CACTCCTCCC ACTTTC fusA_2 85 9.93e-06 GGTATTTTAT CTATCCCCCT TAATCA cds-WP_012048450.1 84 1.37e-05 CTTTTTGTTA TTTTCCTCCT ATATTCC cds-WP_012048431.1 87 1.37e-05 TTATATATCC CTTCCCCACT AAAA cds-WP_003404508.1 85 1.37e-05 CGTATCCGAT ATCTCCTCCT ATCCAG cds-WP_012048355.1 83 1.58e-05 AATTACCTTA AATCCCTCCT TCAGTTGT nusB 87 1.58e-05 TGTATCTTTT AATCCCTCCT TTTA rplK 54 1.97e-05 ACAAAATTAA TCACCCTCCT AAAATTAGGC cds-WP_012048124.1 89 1.97e-05 ATGTTTTTCA CCTCCCTACT TA codY 85 1.97e-05 TTCTCCATTA TCTTCCTCCT TTTGGG cds-WP_012048232.1 85 2.32e-05 AGTTATTACT CAATCCTCCT GAACTT cds-WP_011986653.1 85 2.32e-05 AATTTGTGAT TTCCCCTACT ACGTAG cds-WP_003402124.1 86 2.75e-05 ATATTTTTTG TATTCCCCCT AATTA cds-WP_003358481.1 84 2.75e-05 AATCTTTAAA TTTTCCTCCG TTATATA cds-WP_003357472.1 85 3.11e-05 TATAATTATT TACTCCTCCC AATTCT cds-WP_011987095.1 86 3.67e-05 AAGAGATTTT CTTTCCCACT TCTAT cds-WP_011987038.1 86 4.35e-05 TATTATATTA AATTCCCCCT AGTTA cds-WP_012047704.1 87 4.35e-05 TTAATATACT TACCCCTACT TTTT cds-WP_003399301.1 87 4.35e-05 AATTTAAAAA AATTCCTCCT ATTT rplA 85 4.81e-05 CAATTATGGT GTTTCCTCCT TAATCT cds-WP_003358306.1 87 4.81e-05 TATTTCGTAA TTCCCCCACC GCTA cds-WP_011986476.1 86 5.16e-05 GAAATAGAAT TTCCCCTTCT AAATA cds-WP_012099500.1 86 6.29e-05 TTTATCAATA ATTCCCCACT CGAAA greA_2 86 8.19e-05 CATTGTTTTA TTTCCCCTCT TATCG cds-WP_011986487.1 84 8.19e-05 TCTATTTCTT CTATCCTACT TCTCCCT sigF 38 9.95e-05 AGTAAGTCTT TTCCCCTTCC CTTGATTTTA cds-WP_003356834.1 87 9.95e-05 TATTTTGATG TAATCCTCCG ATTT nusA 81 1.19e-04 TTCCCCTTGA CATTCCTCCA ATTATTTTTT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif YTYYCCTCCT MEME-3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- rpmI 7.8e-08 83_[+3]_7 cds-WP_011986542.1 7.8e-08 21_[+3]_69 rpoC 3.3e-07 83_[+3]_7 rpsI 3.3e-07 84_[+3]_6 rpsF 4.2e-07 80_[+3]_10 rpsS 1.2e-06 83_[+3]_7 fusA 2.4e-06 83_[+3]_7 rplD 2.4e-06 84_[+3]_6 cds-WP_003357370.1 2.4e-06 83_[+3]_7 cds-WP_011986937.1 2.4e-06 21_[+3]_69 cds-WP_012048290.1 3.5e-06 86_[+3]_4 cds-WP_003358234.1 3.5e-06 82_[+3]_8 rplP 4.4e-06 83_[+3]_7 sigH 5.5e-06 86_[+3]_4 cds-WP_003357849.1 5.5e-06 83_[+3]_7 cds-WP_003385301.1 5.5e-06 21_[+3]_69 rpsH 7.1e-06 83_[+3]_7 rpoD 7.1e-06 80_[+3]_10 rplN 8.6e-06 82_[+3]_8 cds-WP_011948365.1 9e-06 84_[+3]_6 fusA_2 9.9e-06 84_[+3]_6 cds-WP_012048450.1 1.4e-05 83_[+3]_7 cds-WP_012048431.1 1.4e-05 86_[+3]_4 cds-WP_003404508.1 1.4e-05 84_[+3]_6 cds-WP_012048355.1 1.6e-05 82_[+3]_8 nusB 1.6e-05 86_[+3]_4 rplK 2e-05 53_[+3]_37 cds-WP_012048124.1 2e-05 88_[+3]_2 codY 2e-05 84_[+3]_6 cds-WP_012048232.1 2.3e-05 84_[+3]_6 cds-WP_011986653.1 2.3e-05 84_[+3]_6 cds-WP_003402124.1 2.8e-05 85_[+3]_5 cds-WP_003358481.1 2.8e-05 83_[+3]_7 cds-WP_003357472.1 3.1e-05 84_[+3]_6 cds-WP_011987095.1 3.7e-05 85_[+3]_5 cds-WP_011987038.1 4.3e-05 85_[+3]_5 cds-WP_012047704.1 4.3e-05 86_[+3]_4 cds-WP_003399301.1 4.3e-05 86_[+3]_4 rplA 4.8e-05 84_[+3]_6 cds-WP_003358306.1 4.8e-05 86_[+3]_4 cds-WP_011986476.1 5.2e-05 85_[+3]_5 cds-WP_012099500.1 6.3e-05 85_[+3]_5 greA_2 8.2e-05 85_[+3]_5 cds-WP_011986487.1 8.2e-05 83_[+3]_7 sigF 9.9e-05 37_[+3]_53 cds-WP_003356834.1 9.9e-05 86_[+3]_4 nusA 0.00012 80_[+3]_10 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif YTYYCCTCCT MEME-3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF YTYYCCTCCT width=10 seqs=47 rpmI ( 84) CTCCCCTCCT 1 cds-WP_011986542.1 ( 22) CTCCCCTCCT 1 rpoC ( 84) CTTCCCTCCT 1 rpsI ( 85) CTTCCCTCCT 1 rpsF ( 81) CACCCCTCCT 1 rpsS ( 84) CTTCCCTCCG 1 fusA ( 84) CTACCCTCCT 1 rplD ( 85) CTTTCCTCCT 1 cds-WP_003357370.1 ( 84) CTACCCTCCT 1 cds-WP_011986937.1 ( 22) TCCCCCTCCT 1 cds-WP_012048290.1 ( 87) ATCCCCCCCT 1 cds-WP_003358234.1 ( 83) TTTCCCCCCT 1 rplP ( 84) CCTTCCTCCT 1 sigH ( 87) ACCCCCCCCT 1 cds-WP_003357849.1 ( 84) TTCTCCTCCT 1 cds-WP_003385301.1 ( 22) TTCTCCCCCT 1 rpsH ( 84) CTTTCCTCCG 1 rpoD ( 81) CTTTCCTCCG 1 rplN ( 83) CTTTCCTCCC 1 cds-WP_011948365.1 ( 85) CACTCCTCCC 1 fusA_2 ( 85) CTATCCCCCT 1 cds-WP_012048450.1 ( 84) TTTTCCTCCT 1 cds-WP_012048431.1 ( 87) CTTCCCCACT 1 cds-WP_003404508.1 ( 85) ATCTCCTCCT 1 cds-WP_012048355.1 ( 83) AATCCCTCCT 1 nusB ( 87) AATCCCTCCT 1 rplK ( 54) TCACCCTCCT 1 cds-WP_012048124.1 ( 89) CCTCCCTACT 1 codY ( 85) TCTTCCTCCT 1 cds-WP_012048232.1 ( 85) CAATCCTCCT 1 cds-WP_011986653.1 ( 85) TTCCCCTACT 1 cds-WP_003402124.1 ( 86) TATTCCCCCT 1 cds-WP_003358481.1 ( 84) TTTTCCTCCG 1 cds-WP_003357472.1 ( 85) TACTCCTCCC 1 cds-WP_011987095.1 ( 86) CTTTCCCACT 1 cds-WP_011987038.1 ( 86) AATTCCCCCT 1 cds-WP_012047704.1 ( 87) TACCCCTACT 1 cds-WP_003399301.1 ( 87) AATTCCTCCT 1 rplA ( 85) GTTTCCTCCT 1 cds-WP_003358306.1 ( 87) TTCCCCCACC 1 cds-WP_011986476.1 ( 86) TTCCCCTTCT 1 cds-WP_012099500.1 ( 86) ATTCCCCACT 1 greA_2 ( 86) TTTCCCCTCT 1 cds-WP_011986487.1 ( 84) CTATCCTACT 1 sigF ( 38) TTCCCCTTCC 1 cds-WP_003356834.1 ( 87) TAATCCTCCG 1 nusA ( 81) CATTCCTCCA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif YTYYCCTCCT MEME-3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 10 n= 27118 bayes= 11.0709 E= 3.9e-028 -106 169 -241 -12 -48 -11 -1220 65 -125 130 -1220 38 -1220 189 -1220 32 -1220 286 -1220 -1220 -1220 286 -1220 -1220 -1220 89 -1220 92 -106 247 -1220 -262 -1220 286 -1220 -1220 -406 -38 -9 96 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif YTYYCCTCCT MEME-3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 10 nsites= 47 E= 3.9e-028 0.170213 0.446809 0.021277 0.361702 0.255319 0.127660 0.000000 0.617021 0.148936 0.340426 0.000000 0.510638 0.000000 0.510638 0.000000 0.489362 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.255319 0.000000 0.744681 0.170213 0.765957 0.000000 0.063830 0.000000 1.000000 0.000000 0.000000 0.021277 0.106383 0.106383 0.765957 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif YTYYCCTCCT MEME-3 regular expression -------------------------------------------------------------------------------- [CT][TA][TC][CT]CC[TC]CCT -------------------------------------------------------------------------------- Time 97.18 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- dnaN 1.40e-02 87_[+2(5.99e-05)]_7 cds-WP_011947911.1 5.28e-01 100 dnaX 2.03e-01 100 cds-WP_003359494.1 3.22e-01 100 cds-WP_003404855.1 2.00e-02 32_[+2(2.71e-05)]_50_[+2(6.54e-06)]_\ 6 cds-WP_011947938.1 5.73e-01 100 cds-WP_011947952.1 9.45e-02 100 cds-WP_003356351.1 3.38e-01 100 rho 2.17e-01 100 rpmE 5.07e-02 100 cds-WP_011947984.1 3.29e-01 100 cds-WP_003356899.1 3.72e-01 100 atpE 6.36e-02 87_[+2(2.71e-05)]_7 cds-WP_003355885.1 4.80e-02 85_[+2(5.99e-05)]_9 cds-WP_011947988.1 6.71e-01 100 atpA 6.75e-01 100 atpG 9.76e-02 89_[+2(4.98e-05)]_5 atpD 9.37e-02 89_[+2(4.98e-05)]_5 cds-WP_003387838.1 5.29e-01 100 cds-WP_011947999.1 9.77e-02 90_[+2(4.98e-05)]_4 cds-WP_003355819.1 7.00e-01 100 rpoN 9.93e-02 78_[+2(5.19e-05)]_16 cds-WP_003399034.1 1.41e-01 29_[+2(8.60e-05)]_65 cds-WP_003390961.1 3.94e-01 100 cds-WP_011948050.1 5.72e-01 100 cds-WP_011948062.1 1.31e-01 100 cds-WP_011948063.1 9.75e-02 100 cds-WP_011948072.1 7.05e-01 100 cds-WP_003355791.1 3.44e-01 100 cds-WP_011948077.1 1.08e-01 88_[+2(5.99e-05)]_6 cds-WP_003362768.1 1.69e-01 100 cds-WP_011948118.1 3.57e-02 85_[+2(2.71e-05)]_9 cds-WP_003362795.1 3.27e-01 100 cds-WP_011948172.1 2.48e-01 100 cds-WP_011948175.1 2.20e-02 85_[+2(6.54e-06)]_9 cds-WP_003355838.1 2.23e-02 100 cds-CBO_RS18635 8.03e-01 100 cds-WP_011948219.1 6.12e-02 89_[+2(2.71e-05)]_5 cds-WP_003359683.1 4.35e-01 100 cds-WP_011948232.1 2.98e-01 100 cds-WP_003359806.1 3.04e-02 87_[+1(4.63e-05)]_5 cds-WP_011986143.1 7.02e-01 100 cds-WP_003403434.1 9.31e-02 88_[+2(4.98e-05)]_6 cds-WP_011948324.1 5.27e-01 100 cds-WP_011948327.1 3.44e-01 100 cds-WP_011948333.1 3.45e-01 100 cds-WP_011948348.1 5.69e-01 100 cds-WP_003356776.1 8.28e-03 84_[+1(7.06e-05)]_8 cds-WP_011948365.1 3.05e-04 84_[+3(8.99e-06)]_6 cds-WP_011948369.1 1.14e-01 88_[+2(6.64e-05)]_6 cds-WP_011948372.1 5.34e-03 89_[+2(6.54e-06)]_5 cds-WP_011948378.1 2.97e-02 90_[+2(4.98e-05)]_4 greA 5.60e-02 84_[+2(2.71e-05)]_10 cds-WP_230869867.1 2.63e-02 36_[+2(2.71e-05)]_58 cds-WP_225900976.1 2.32e-01 100 cds-WP_011948438.1 3.01e-02 88_[+2(2.71e-05)]_6 cds-WP_011948452.1 1.12e-03 85_[+1(2.88e-05)]_7 cds-WP_011948453.1 1.73e-01 100 cds-WP_011948466.1 6.63e-03 88_[+2(6.54e-06)]_6 cds-WP_003387694.1 5.81e-02 89_[+2(2.71e-05)]_5 cds-WP_011948471.1 2.46e-01 100 cds-WP_011948534.1 4.13e-02 87_[+2(2.71e-05)]_7 cds-WP_011948541.1 5.72e-01 100 cds-WP_011948545.1 9.12e-02 100 cds-WP_011948547.1 9.58e-02 70_[+2(4.98e-05)]_11_[+2(4.98e-05)]_\ 7 cds-WP_003399301.1 3.84e-03 86_[+3(4.35e-05)]_4 cds-WP_003357080.1 1.74e-02 85_[+1(5.66e-05)]_7 cds-WP_011948557.1 9.74e-02 79_[+2(4.98e-05)]_15 cds-WP_011948563.1 1.53e-02 88_[+2(6.54e-06)]_6 cds-WP_011948567.1 1.47e-02 100 cds-WP_011948570.1 4.99e-02 82_[+2(2.71e-05)]_12 cds-WP_079995886.1 6.85e-03 87_[+2(6.54e-06)]_7 cds-WP_011948597.1 9.12e-02 87_[+2(4.98e-05)]_7 cds-WP_011948600.1 1.26e-02 85_[+1(4.63e-05)]_7 cds-WP_011948616.1 7.47e-01 100 cds-WP_011948628.1 5.98e-02 87_[+2(2.71e-05)]_7 cds-WP_011948668.1 6.36e-02 90_[+2(2.71e-05)]_4 cds-WP_011948696.1 5.20e-01 100 cds-WP_003356907.1 5.73e-01 100 cds-WP_011948703.1 3.44e-01 100 cds-WP_003356424.1 9.06e-01 100 cds-WP_011948759.1 6.36e-02 90_[+2(2.71e-05)]_4 cds-WP_011948763.1 5.83e-02 86_[+2(2.71e-05)]_8 cds-WP_011948772.1 6.75e-01 100 rpsA 7.91e-01 100 cds-WP_003356138.1 5.71e-01 100 cds-WP_011948833.1 6.34e-02 87_[+2(2.71e-05)]_7 cds-WP_011948840.1 1.24e-01 100 cds-WP_011948844.1 6.37e-01 100 cds-WP_003356834.1 1.69e-02 86_[+3(9.95e-05)]_4 cds-WP_011948871.1 1.82e-02 87_[+2(6.54e-06)]_7 mtnA 6.36e-02 88_[+2(2.71e-05)]_6 cds-WP_011948894.1 1.39e-01 90_[+2(8.60e-05)]_4 cds-WP_003358748.1 5.63e-02 100 cds-WP_003358712.1 4.49e-01 100 cds-WP_011948948.1 7.07e-01 100 ychF 6.74e-01 100 cds-WP_003393623.1 5.29e-01 100 cds-WP_003358553.1 1.90e-01 100 cds-WP_011949080.1 5.76e-02 89_[+2(2.71e-05)]_5 cds-WP_003388928.1 4.35e-01 100 cds-WP_011949087.1 3.16e-01 100 cds-WP_011949091.1 6.34e-02 89_[+2(2.71e-05)]_5 cds-CBO_RS07675 6.03e-01 100 cds-WP_011949098.1 1.33e-02 100 cds-WP_011949106.1 7.07e-01 100 cds-WP_011949120.1 7.81e-03 100 cds-WP_011949137.1 6.86e-01 100 cds-WP_011949138.1 7.07e-01 100 cds-WP_011986272.1 2.71e-01 100 cds-WP_011949150.1 3.15e-01 100 cds-WP_011949159.1 7.07e-01 100 cds-WP_011986282.1 4.01e-01 100 cds-WP_011986286.1 5.01e-01 100 cds-CBO_RS08185 6.74e-02 15_[+2(8.60e-05)]_79 cds-WP_164928177.1 2.28e-01 100 cds-WP_012047595.1 8.48e-02 100 cds-WP_003395988.1 1.19e-01 24_[+2(6.64e-05)]_70 cds-WP_011986310.1 4.31e-01 100 cds-WP_011986315.1 5.55e-01 100 lexA 5.42e-01 100 cds-WP_003392901.1 2.04e-02 86_[+2(6.54e-06)]_8 cds-WP_012047676.1 2.74e-01 100 cds-WP_003358959.1 5.56e-01 100 scpB 1.92e-01 100 nusB 4.10e-04 86_[+3(1.58e-05)]_4 efp 1.42e-02 85_[+1(5.66e-05)]_7 cds-WP_003358480.1 6.36e-02 89_[+2(2.71e-05)]_5 cds-WP_011986476.1 1.92e-02 85_[+3(5.16e-05)]_5 cds-WP_011986487.1 7.22e-03 83_[+3(8.19e-05)]_7 cds-WP_011986494.1 2.01e-01 100 cds-WP_011986498.1 6.92e-01 100 cds-WP_003385301.1 4.35e-04 21_[+3(5.51e-06)]_52_[+3(7.35e-05)]_\ 7 treR 8.37e-01 100 cds-WP_012047704.1 8.80e-03 86_[+3(4.35e-05)]_4 cds-WP_003358481.1 7.93e-04 83_[+3(2.75e-05)]_7 cds-WP_011986542.1 3.75e-06 21_[+3(7.82e-08)]_69 cds-WP_011986544.1 2.46e-01 100 cds-WP_011986554.1 5.64e-01 100 cds-WP_011986562.1 6.49e-03 88_[+1(7.06e-05)]_4 cds-WP_003358306.1 9.12e-04 86_[+3(4.81e-05)]_4 cds-WP_003384878.1 6.35e-02 100 cds-WP_011986616.1 2.44e-01 100 cds-WP_003402124.1 6.72e-03 85_[+3(2.75e-05)]_5 cds-WP_003358234.1 1.65e-04 82_[+3(3.49e-06)]_8 cds-WP_011986653.1 1.28e-02 84_[+3(2.32e-05)]_6 cds-WP_011986682.1 3.42e-01 100 cds-WP_011986684.1 2.89e-01 100 cds-WP_012047750.1 7.50e-02 100 cds-WP_012047752.1 1.19e-01 100 cds-WP_003391706.1 3.27e-02 100 cds-WP_003358274.1 4.04e-01 100 cds-WP_011986719.1 1.04e-02 86_[+2(2.71e-05)]_8 cds-WP_011986731.1 7.42e-02 100 cds-WP_011986754.1 7.05e-01 100 cds-WP_011986758.1 7.60e-02 100 cds-WP_011986765.1 1.09e-01 100 cds-WP_003395350.1 1.71e-03 86_[+1(6.85e-06)]_6 cds-WP_011986767.1 1.58e-01 100 cds-WP_011986769.1 4.66e-01 100 cds-WP_156226176.1 3.51e-01 100 cds-WP_012047775.1 7.00e-03 100 cds-WP_041350636.1 5.41e-01 100 cds-WP_341349816.1 2.01e-03 70_[+1(3.81e-06)]_22 cds-WP_012047848.1 5.78e-02 87_[+2(4.98e-05)]_7 cds-WP_012047850.1 2.15e-01 100 rpsO 1.95e-02 86_[+1(4.63e-05)]_6 infB 2.98e-02 100 cds-WP_004440225.1 3.48e-01 100 cds-WP_003388362.1 1.25e-01 100 nusA 3.20e-03 83_[+1(7.06e-05)]_9 cds-WP_011986794.1 2.01e-03 88_[+1(2.88e-05)]_4 tsf 4.10e-04 86_[+1(2.88e-05)]_6 rpsB 3.77e-03 87_[+1(1.47e-05)]_5 codY 4.13e-04 84_[+3(1.97e-05)]_6 rplS 5.94e-05 85_[+1(6.85e-06)]_7 rpsP 5.82e-04 86_[+1(3.81e-06)]_6 rpmF 2.78e-04 86_[+1(3.81e-06)]_6 prdR 5.91e-02 100 rpmB 8.32e-02 86_[+2(4.98e-05)]_8 rpoZ 8.18e-04 85_[+1(2.88e-05)]_7 cds-WP_257262151.1 1.00e+00 100 nrdR 2.25e-02 100 sigG 5.03e-01 100 sigE 2.91e-04 87_[+1(6.85e-06)]_5 sigK 6.09e-04 86_[+1(1.81e-05)]_6 cds-WP_003391911.1 2.23e-02 100 cds-WP_011986902.1 6.04e-04 85_[+1(3.81e-06)]_7 cds-WP_011986903.1 1.94e-01 100 cds-WP_011986937.1 5.53e-06 21_[+3(2.37e-06)]_55_[+1(1.81e-05)]_\ 6 cds-WP_003404508.1 1.63e-03 84_[+3(1.37e-05)]_6 cds-WP_011986984.1 3.48e-02 100 rfbF 4.49e-03 86_[+1(2.01e-05)]_6 cds-WP_011987038.1 1.20e-03 62_[+3(6.29e-05)]_13_[+3(4.35e-05)]_\ 5 cds-WP_011987040.1 1.72e-01 100 cds-WP_011987070.1 1.89e-02 87_[+1(5.66e-05)]_5 cds-WP_011987090.1 3.81e-01 100 cds-WP_011987095.1 1.28e-02 85_[+3(3.67e-05)]_5 cds-WP_011987106.1 5.30e-02 100 cds-WP_011987107.1 5.60e-02 88_[+2(2.71e-05)]_6 cds-WP_012047951.1 4.67e-01 100 cds-WP_012047976.1 4.55e-01 100 rpoD 2.83e-03 80_[+3(7.10e-06)]_10 rpsU 1.98e-05 83_[+3(3.92e-06)]_7 prmA 8.22e-04 86_[+1(2.88e-05)]_6 hrcA 4.52e-02 100 rpsT 5.29e-02 88_[+2(7.37e-05)]_6 holA 8.59e-02 100 selB 6.84e-01 100 cds-WP_003357849.1 6.95e-04 83_[+3(5.51e-06)]_7 cds-WP_012048020.1 1.81e-01 100 rpmA 5.03e-04 87_[+1(3.81e-06)]_5 cds-WP_012048022.1 8.96e-01 100 rplU 1.42e-04 86_[+1(3.81e-06)]_6 polA 2.26e-01 100 cds-WP_012099500.1 2.75e-02 85_[+3(6.29e-05)]_5 cds-WP_012048067.1 3.44e-01 100 cds-WP_012048092.1 1.01e-01 100 sigF 1.52e-02 37_[+3(9.95e-05)]_53 cds-WP_012048124.1 7.49e-04 88_[+3(1.97e-05)]_2 rplT 1.37e-03 85_[+1(1.47e-05)]_7 rpmI 1.40e-06 83_[+3(7.82e-08)]_7 infC 6.65e-01 100 cds-WP_003357340.1 5.33e-01 100 cds-WP_012048183.1 1.51e-02 100 cds-WP_003357370.1 8.22e-05 83_[+3(2.37e-06)]_7 cds-WP_012048201.1 6.14e-02 100 cds-WP_012048232.1 2.03e-03 84_[+3(2.32e-05)]_6 cds-WP_012048290.1 1.14e-04 86_[+3(3.49e-06)]_4 cds-WP_012048304.1 1.48e-02 100 cds-WP_003360267.1 2.04e-03 85_[+1(1.47e-05)]_7 rpsD 1.11e-03 89_[+1(2.88e-05)]_3 cds-WP_012048331.1 1.90e-01 100 cds-WP_012048343.1 6.97e-01 100 rpsI 1.52e-04 84_[+3(3.28e-07)]_6 rplM 1.42e-04 87_[+1(2.01e-05)]_5 rplQ 1.09e-03 84_[+1(1.47e-05)]_8 cds-WP_003357472.1 1.75e-04 84_[+3(3.11e-05)]_6 rpsD_2 1.75e-05 83_[+1(3.81e-06)]_9 rpsK 1.02e-04 87_[+1(6.85e-06)]_5 rpsM 4.92e-03 83_[+1(3.81e-06)]_9 rpmJ 1.08e-05 86_[+1(1.07e-06)]_6 infA 5.58e-03 82_[+1(7.06e-05)]_10 cds-WP_003357464.1 1.23e-01 100 rplO 4.12e-05 85_[+1(3.81e-06)]_7 rpmD 1.65e-03 85_[+1(1.47e-05)]_7 rpsE 1.61e-04 87_[+1(6.85e-06)]_5 rplR 1.05e-02 100 rplF 6.30e-04 86_[+1(3.81e-06)]_6 rpsH 1.14e-04 83_[+3(7.10e-06)]_7 cds-WP_003357636.1 3.34e-04 87_[+1(6.85e-06)]_5 rplE 5.81e-04 86_[+1(1.47e-05)]_6 rplX 5.27e-04 84_[+1(3.81e-06)]_8 rplN 2.92e-04 82_[+3(8.56e-06)]_8 rpsQ 5.38e-04 83_[+3(3.11e-05)]_7 rpmC 4.10e-02 100 rplP 2.23e-05 83_[+3(4.36e-06)]_7 rpsC 3.76e-05 87_[+1(6.85e-06)]_5 rplV 5.56e-04 85_[+1(1.47e-05)]_7 rpsS 2.25e-04 83_[+3(1.25e-06)]_7 rplB 2.29e-04 87_[+1(6.85e-06)]_5 rplW 5.70e-04 84_[+1(3.81e-06)]_8 rplD 2.47e-04 84_[+3(2.37e-06)]_6 rplC 2.70e-04 85_[+1(3.81e-06)]_7 rpsJ 4.67e-05 85_[+1(6.85e-06)]_7 tuf 2.83e-04 83_[+3(1.37e-05)]_7 fusA 7.71e-05 83_[+3(2.37e-06)]_7 rpsG 2.49e-04 86_[+1(6.85e-06)]_6 rpsL 6.30e-04 87_[+1(3.81e-06)]_5 cds-WP_012048355.1 1.52e-04 82_[+3(1.58e-05)]_8 rpoC 1.42e-04 83_[+3(3.28e-07)]_7 rpoB 3.85e-02 100 rplL 2.96e-02 84_[+1(4.63e-05)]_8 rplJ 9.11e-05 84_[+1(3.81e-06)]_8 rplA 3.89e-04 60_[+1(3.15e-05)]_19_[+1(2.88e-05)]_\ 5 rplK 2.64e-05 53_[+3(1.97e-05)]_23_[+1(3.81e-06)]_\ 6 nusG 6.32e-05 65_[+1(6.85e-06)]_27 rpmG 9.40e-04 86_[+1(3.81e-06)]_6 tuf_2 6.09e-05 83_[+3(1.37e-05)]_7 sigH 4.48e-04 86_[+3(5.51e-06)]_4 cds-WP_003357349.1 4.60e-01 100 fusA_2 1.75e-03 84_[+3(9.93e-06)]_6 greA_2 3.13e-02 85_[+3(8.19e-05)]_5 cds-WP_003359441.1 2.00e-02 86_[+1(5.66e-05)]_6 cds-WP_003359471.1 7.16e-05 3_[+3(8.19e-05)]_69_[+1(1.81e-05)]_\ 10 mfd 8.82e-02 100 cds-WP_012048397.1 5.53e-02 100 cds-WP_003400977.1 9.77e-02 87_[+2(4.98e-05)]_7 cds-WP_003359449.1 9.39e-02 88_[+2(4.98e-05)]_6 cds-WP_003359341.1 6.26e-02 100 cds-WP_012048431.1 2.00e-03 86_[+3(1.37e-05)]_4 rplI 3.17e-02 100 rpsR 1.33e-05 87_[+1(6.85e-06)]_5 rpsF 2.89e-07 80_[+3(4.21e-07)]_10 cds-WP_012048450.1 6.04e-04 83_[+3(1.37e-05)]_7 noc 1.07e-02 100 rpmH 3.68e-04 84_[+1(3.81e-06)]_8 cds-WP_011949166.1 9.97e-01 100 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (3) found. ******************************************************************************** CPU: kodomo ********************************************************************************