******************************************************************************** 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_038608981.1 1.0000 100 cds-WP_051952093.1 1.0000 100 cds-WP_038609051.1 1.0000 100 cds-WP_038609173.1 1.0000 100 cds-WP_038609175.1 1.0000 100 cds-WP_038609209.1 1.0000 100 cds-WP_038609252.1 1.0000 100 cds-WP_038609318.1 1.0000 100 cds-WP_201773347.1 1.0000 100 cds-WP_038609473.1 1.0000 100 cds-WP_038609482.1 1.0000 100 cds-WP_070475253.1 1.0000 100 cds-WP_038609525.1 1.0000 100 cds-WP_038609549.1 1.0000 100 nusG 1.0000 100 rplK 1.0000 100 rplA 1.0000 100 rplJ 1.0000 100 rplL 1.0000 100 cds-WP_038609586.1 1.0000 100 cds-WP_038609589.1 1.0000 100 rpsL 1.0000 100 rpsG 1.0000 100 fusA 1.0000 100 tuf 1.0000 100 rpsJ 1.0000 100 rplC 1.0000 100 rplD 1.0000 100 rplW 1.0000 100 rplB 1.0000 100 rpsS 1.0000 100 rplV 1.0000 100 rpsC 1.0000 100 rplP 1.0000 100 rpmC 1.0000 100 rpsQ 1.0000 100 rplN 1.0000 100 rplX 1.0000 100 rplE 1.0000 100 rpsH 1.0000 100 rplF 1.0000 100 rplR 1.0000 100 rpsE 1.0000 100 rpmD 1.0000 100 rplO 1.0000 100 infA 1.0000 100 rpsM 1.0000 100 rpsK 1.0000 100 rpsD 1.0000 100 cds-WP_038609724.1 1.0000 100 rplQ 1.0000 100 rplM 1.0000 100 rpsI 1.0000 100 cds-WP_038609794.1 1.0000 100 cds-WP_051952129.1 1.0000 100 cds-WP_051952132.1 1.0000 100 cds-WP_038609828.1 1.0000 100 cds-WP_038609850.1 1.0000 100 cds-WP_038609897.1 1.0000 100 cds-WP_038609911.1 1.0000 100 cds-WP_038609974.1 1.0000 100 cds-WP_038609977.1 1.0000 100 cds-WP_051952377.1 1.0000 100 cds-WP_038610090.1 1.0000 100 cds-WP_051952161.1 1.0000 100 cds-WP_038610183.1 1.0000 100 cds-WP_038610255.1 1.0000 100 cds-WP_051952175.1 1.0000 100 cds-WP_038610359.1 1.0000 100 cds-WP_038610377.1 1.0000 100 cds-WP_038610483.1 1.0000 100 rpsR 1.0000 100 rpsN 1.0000 100 rpmG 1.0000 100 rpmB 1.0000 100 cds-WP_034999480.1 1.0000 100 cds-WP_038610531.1 1.0000 100 cds-WP_084768153.1 1.0000 100 cds-WP_084768154.1 1.0000 100 cds-WP_038610687.1 1.0000 100 cds-WP_051952190.1 1.0000 100 mfd 1.0000 100 greA 1.0000 100 cds-WP_051952193.1 1.0000 100 ychF 1.0000 100 cds-WP_034666346.1 1.0000 100 cds-WP_004601215.1 1.0000 100 cds-WP_005290994.1 1.0000 100 cds-WP_038610879.1 1.0000 100 cds-WP_051952203.1 1.0000 100 sigE 1.0000 100 cds-WP_038611038.1 1.0000 100 cds-WP_051952212.1 1.0000 100 cds-WP_038611046.1 1.0000 100 rho 1.0000 100 cds-WP_038611081.1 1.0000 100 atpB 1.0000 100 cds-WP_034999811.1 1.0000 100 cds-WP_038611094.1 1.0000 100 cds-WP_038611097.1 1.0000 100 atpA 1.0000 100 cds-WP_038611103.1 1.0000 100 atpD 1.0000 100 cds-WP_038611109.1 1.0000 100 cds-WP_038611166.1 1.0000 100 cds-WP_069202889.1 1.0000 100 cds-WP_144242416.1 1.0000 100 cds-WP_038611277.1 1.0000 100 cds-WP_038611327.1 1.0000 100 cds-WP_038611336.1 1.0000 100 polA 1.0000 100 rpsA 1.0000 100 infC 1.0000 100 rpmI 1.0000 100 rplT 1.0000 100 cds-WP_038611461.1 1.0000 100 cds-WP_051952230.1 1.0000 100 cds-WP_038611481.1 1.0000 100 cds-WP_038611542.1 1.0000 100 cds-WP_038611544.1 1.0000 100 cds-WP_144242426.1 1.0000 100 cds-WP_236627161.1 1.0000 100 cds-WP_038611639.1 1.0000 100 cds-WP_051952243.1 1.0000 100 rpoZ 1.0000 100 nusB 1.0000 100 efp 1.0000 100 ppgK 1.0000 100 cds-WP_038611916.1 1.0000 100 cds-WP_038611925.1 1.0000 100 cds-WP_038611927.1 1.0000 100 cds-WP_038611949.1 1.0000 100 nrdR 1.0000 100 lexA 1.0000 100 cds-WP_038611961.1 1.0000 100 cds-WP_051952258.1 1.0000 100 rpsO 1.0000 100 infB 1.0000 100 cds-WP_038612104.1 1.0000 100 nusA 1.0000 100 tsf 1.0000 100 rpsB 1.0000 100 rplS 1.0000 100 cds-WP_038612197.1 1.0000 100 rpsP 1.0000 100 cds-WP_038612278.1 1.0000 100 cds-WP_038612284.1 1.0000 100 dnaE 1.0000 100 cds-WP_038612328.1 1.0000 100 cds-WP_038614247.1 1.0000 100 cds-WP_051952295.1 1.0000 100 hrcA 1.0000 100 rpsT 1.0000 100 holA 1.0000 100 rpmA 1.0000 100 rplU 1.0000 100 cds-WP_051952305.1 1.0000 100 cds-WP_038612873.1 1.0000 100 ykgO 1.0000 100 cds-WP_201773330.1 1.0000 100 cds-WP_038612979.1 1.0000 100 cds-WP_038612998.1 1.0000 100 cds-WP_038614395.1 1.0000 100 cds-WP_051952332.1 1.0000 100 cds-WP_038613260.1 1.0000 100 cds-WP_038613274.1 1.0000 100 cds-WP_084768332.1 1.0000 100 cds-WP_038613314.1 1.0000 100 cds-WP_038613354.1 1.0000 100 cds-WP_051952347.1 1.0000 100 cds-WP_038613381.1 1.0000 100 cds-WP_038613390.1 1.0000 100 cds-WP_236627210.1 1.0000 100 rplI 1.0000 100 rpsF 1.0000 100 cds-WP_038613525.1 1.0000 100 cds-WP_051952429.1 1.0000 100 cds-WP_038613532.1 1.0000 100 cds-WP_038613537.1 1.0000 100 cds-WP_051952161.1-2 1.0000 100 cds-WP_038610183.1-2 1.0000 100 cds-WP_038610255.1-2 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 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= 183 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= 18300 N= 183 sample: seed= 0 hsfrac= 0 searchsize= 18300 norand= no csites= 1000 Letter frequencies in dataset: A 0.211 C 0.298 G 0.297 T 0.194 Background letter frequencies (from file dataset with add-one prior applied): A 0.211 C 0.298 G 0.297 T 0.194 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF CSDCRMGVBCVBCGWCNHSVTSRNSVHSRTCSMSSDYGHSRHSDHSBMGM MEME-1 width = 50 sites = 48 llr = 540 E-value = 3.4e-007 ******************************************************************************** -------------------------------------------------------------------------------- Motif CSDCRMGVBCVBCGWCNHSVTSRNSVHSRTCSMSSDYGHSRHSDHSBMGM MEME-1 Description -------------------------------------------------------------------------------- Simplified A :13:44:21:41:24:22:33:33:331321142:3113153124::424 pos.-specific C 9316:323372262183342261274452183353141452432343323 probability G 14425164432325123144:45233134215235426143154143161 matrix T :13222123:14124:23215:13::3215::1113312:12122241:1 bits 2.4 2.1 1.9 1.7 Relative 1.4 Entropy 1.2 * (16.2 bits) 0.9 * * * * 0.7 * * * ** * * 0.5 * ** * * * ** ** * ** * * * 0.2 ******* ***** ** ** ******** ************** ****** 0.0 -------------------------------------------------- Multilevel CGGCGAGGGCATCGACCTCGTCGTCCCCGTCGACGGCGCCACGGAGTAGA consensus CT ACCCCGCGG T GCGAAGAAGGAGAG CCGCAT AGGACACCGCAC sequence A T GC ATCC C AT T T CT TT C C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CSDCRMGVBCVBCGWCNHSVTSRNSVHSRTCSMSSDYGHSRHSDHSBMGM MEME-1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------------------------------------------------- rplB 10 3.27e-14 CGTCACTCT CCGCGAGGGCAGCGACTCCATCGACATCTTCGGGGGTGCGACGGCCTAAC GGCTATCGCA rplQ 6 2.76e-10 TACGA CGCCGAGACCGGGGACTATGTCGACACCAGCGCGGACGAGACCGAGTAAC ACAACAGAGC rplC 17 1.32e-09 CGGTGGACGC GCTCATGCGCATCGACCTGCCGGCCAGCGTCGACGTGAACATCCAGTAGA GCAATCCCCA rplO 45 8.54e-09 GCGGCCAGAT CCTCAAGGTGCGCCACCTCGTCACCGTTGAAGAAGTTGCAGGGGAGTAGA TACCAC cds-WP_038611094.1 4 3.63e-08 CTT CGTTGAGGCGCTCGCCCTCATCGGCCTCGTTGCCGGCTTCCTGTTCTAAA AAGCGTCCGC rplE 33 4.12e-08 CGACCCGCGT CGGCTACCGCTTCGACGAGGACGGCAAGAAGGTCCGCGTGGCCAAGTCGA ACGGGAAGGA rplD 11 1.74e-07 TCGACGGCGA CAACAACCTCATCCTGATCAAGGGCGCCATCCCGGGTGCCAAGGGTTCCG TTGTTACCGT cds-WP_038610255.1 38 2.45e-07 TCTTCAGCGG CAGCGGCAGCAGCTACGTCATGGGCAAGGCCGAAGACACCACAGATTCGG ACTGGGAGTT rplV 7 2.45e-07 GTTCAT CGATGAGTCCATGGTCGGCCACAAGCTCGGCGAGTTTGCACCGACCAAGA CCTTCAAGGG cds-WP_038609175.1 7 2.74e-07 CATGGA CGGCGTGGCCACTTGCGTGCTGCTCGCCTGCGTTGAGGCGGCGGAGGCGA ACGAGGGCTA cds-WP_038611461.1 4 3.82e-07 CGA CGTGGCGTGGACCGGCCTTGACGTGGACCCGGCCGTTGTCGCGGCCTCGA ATTGGACGTA cds-WP_038611097.1 35 3.82e-07 ATTCGACCCG CCGCTCGAACACGATCGACGAGTTCCTAAGCGAGCTCGACCACGTGTCGA CGAGGAAGTA cds-WP_038611109.1 29 4.26e-07 CGGAGCAGGC CTTCAACGGCCTTGGCGGTCTGGACGATGTCGAGGCTGCGTACAAGAAGC TGCAGGCGTA cds-WP_038612979.1 32 5.29e-07 CGTCGATAGC CACCGTGCGCCTCGACGACGTCGACGCCATGGCCGAGTTCCTTGCCCAGC TCGCAGACGA rpsG 6 6.54e-07 GTGCG CTACAAGATCATCCGCGGCGCGCTGGATACCCAGGGTGTGAAGGACCGCA AGCAGGCACG cds-WP_236627210.1 49 7.26e-07 AAGCGCAGTG CCTGTGGCTGATTGACCCTGTCTACGCCGACAAGGACGGGAAGTAGCCCA AC cds-WP_038610255.1-2 29 8.06e-07 TAGAGCTCGT GGTGGGCTTCATCTTCTTTCTCGTCCCTTACAACATTGCGATGTATGGGA TAAACGACGT rpsN 28 8.06e-07 CGTTGTTGGG CCTGGCGTAGTGCAACTTCTTCATGCTGGGCCAACACGCGTTCGTGCAGC TTAAGGCGCT rplS 36 1.21e-06 TGTGCTTGGC CGGCTCGCGGGGCGTCCCCTTCACGGCGGTCCCAGGAGACAGGCTTGTGC ATTTCCTAAC cds-WP_038611327.1 19 1.34e-06 CGCCAGATCG CGTTGCCGTCGGTCTCCGGATGGGCCCCGTCAATTGAGCGAAAGTGTTGA CAGAATGTTG rplX 49 1.34e-06 GTGAGCTGCG CGACAAGCGCTTCATGAAGATCGTGTCTCTCGCACCGGAGGTGATCTAAC CT cds-WP_084768154.1 20 1.48e-06 CCGATCTATT CCGCGACGGCTTGGACCTGTAGCTCCCCCTCTTCGAGGTGGCGCCCGTAA GCGTCTGCTG cds-WP_038609589.1 20 1.48e-06 CGCCTAAGCG CCAGGTAGCCGTCGTCAAGCACTTGCTTTACGACGGCACGACGAACGAAC AGCACATACC cds-WP_051952161.1-2 44 1.64e-06 ACTTAATGTT CTTCATTTCCACCGTTGTTGTCATCCCCGACCCCTTAGACACCTACCCCC GGGAAAA rpsI 2 1.64e-06 C CCGTCAGTCCATCAAGAAGCTGCACGTCTTCGTCGGTGCCGAGCACCCGT ACGCTGGCCA cds-WP_038611103.1 1 1.99e-06 . CGACTCGAGCACCGTCGGCAAGAACCAGCTCAAAGTCAGCCGCTCCTAGT CCGCGCGCAA cds-WP_034999811.1 34 2.42e-06 AACTGAATAA CCCCACTATCTGTCACTTGCTCACCCGCATCCCGCGGGAGAGCGCCTAGA AAGGGAACGA rplP 11 2.42e-06 TCCGAAGAAC GAGCGCGGTGGCCGTGGCGACCGTGACCGTCGTCCGCGCCGCGGCGGCCA GCGCCGTCAG cds-WP_038610183.1-2 23 2.66e-06 GCCGCAGCTT CGACAACGTCCGCGACACCGCCCGCAAACGCGGCGTCGCCCTCCCGGACC TCTCCCGCCA cds-WP_038610531.1 6 2.93e-06 GCCAA CGCCATGGTCCACCTCCCGGAGGACGCGATCCACGTTCGCCCCGGCGACA TTGTGGATGT rpsK 49 3.53e-06 AGACCAACGC GCGCACCCGCAAGGGCCCGAAGAAGACCATCGCAGGAAAGAAGAAGTAAC CT nusB 26 5.57e-06 AGGTCCAAGG CGACAAGAACCTCTGCCCGTTGCACCAGTTCCACCTGTGGGCGTGGCCGC TGATGGACAG cds-WP_038610359.1 38 7.27e-06 TCCGATTGGA CGATGAGCGGGCCGTCGCCGAGAGCCATGTGGAGTACTCCTCAAGGTTGG TAGCGTGGCC rpsC 44 7.27e-06 CATTCCAGAT CCGGAAGCGCACCTCCCACATCACCGTTGTTGTCGAGTCCAAGGAAGGGG CCAAGTA nusA 18 7.94e-06 ACTCAAGTTG CGCGGCGACCGTCGTCTTTGCGACGACCGCCTGGCACGTAAACTTCTAGA ACTCCGGCGA atpA 14 8.66e-06 TCCGTGTGGG CGATGAGGTCATCGACGGTTCGACGCGCGGCAAACTTGACCGCCTTCGGA CCGACATGGC cds-WP_038610879.1 13 8.66e-06 TCCAGCGCGT CCGAGCGCTCAGCATCGCCCACGCGAATCTCGTCCATCACAGCTCCCAAC TTGCACTTGC rpmC 41 9.44e-06 AGGCGCTGCG CCGCGCTGGCGCGAAGCTGCCCTGCAAGGTCCGCGTGATCAAGAAGGAGG ACCAGTTCTA cds-WP_038612278.1 47 1.12e-05 TGGACACTCC CTGTGAGGACGCGCACAACCTGGACCCCGGCGGCTGCCCGTCTATGTTGA ACTT cds-WP_144242416.1 10 1.56e-05 TCTGGATGT GCGCATGTGGCGTTACTCTATCGCGCAGTACCGCTATGCCACACTTCCGC ATCGCTTGCT cds-WP_038611949.1 4 1.99e-05 AAA CTGGTTTCGGGGTTTGTCTGTGGACGCGATCCAGTATGACACAGATGTAG CCCGCTTTCA rplW 13 2.95e-05 TCGTGTTCTC GGTTGAGGCGCTGCACACCTTCATCAACCGCGGCAATGTCGTGGCTGCAG CTGCCGGCGC rpsQ 14 3.18e-05 CCGTGAAGCG CGACATCGCGCGCATCTACACGGTGCTGCGCGAGCGCGAGCTTGGCCTGT CCGTCGTCCC rpsS 33 3.18e-05 GCAACCCGAA CCGTTATTCCAACAACATGATCGTGCGGCGCCGCCGCTCGAAGAAGCGCT AAGAGGAGGT cds-WP_038614247.1 33 3.43e-05 GAAGAGGACC CTGCACGAGCCGCTGGCCGATCGTCGCAATACGCCCCGCCGCGTCGGCCC CCCGATCTGA rpmA 8 4.63e-05 TGTTCTT GTTCTGGCCGATGTTCCAGGCGGTCCCAGTGGCGGTCGTCGTCTGGTGGC AGTTCTAGTG cds-WP_038614395.1 1 6.64e-05 . CGTCACCGGCGGCACCACCGCCTGGGTGGAACAAGGCTTGCCCCACCAAA GTTAGGAAGC cds-WP_038609252.1 16 6.64e-05 ATACCTGGGG CGAGGATGGCTGGGAGCTCGTCGCCGTCACGCCTGGTCCGACGCAAGACA ACGTGGTCGC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CSDCRMGVBCVBCGWCNHSVTSRNSVHSRTCSMSSDYGHSRHSDHSBMGM MEME-1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- rplB 3.3e-14 9_[+1]_41 rplQ 2.8e-10 5_[+1]_45 rplC 1.3e-09 16_[+1]_34 rplO 8.5e-09 44_[+1]_6 cds-WP_038611094.1 3.6e-08 3_[+1]_47 rplE 4.1e-08 32_[+1]_18 rplD 1.7e-07 10_[+1]_40 cds-WP_038610255.1 2.5e-07 37_[+1]_13 rplV 2.5e-07 6_[+1]_44 cds-WP_038609175.1 2.7e-07 6_[+1]_44 cds-WP_038611461.1 3.8e-07 3_[+1]_47 cds-WP_038611097.1 3.8e-07 34_[+1]_16 cds-WP_038611109.1 4.3e-07 28_[+1]_22 cds-WP_038612979.1 5.3e-07 31_[+1]_19 rpsG 6.5e-07 5_[+1]_45 cds-WP_236627210.1 7.3e-07 48_[+1]_2 cds-WP_038610255.1-2 8.1e-07 28_[+1]_22 rpsN 8.1e-07 27_[+1]_23 rplS 1.2e-06 35_[+1]_15 cds-WP_038611327.1 1.3e-06 18_[+1]_32 rplX 1.3e-06 48_[+1]_2 cds-WP_084768154.1 1.5e-06 19_[+1]_31 cds-WP_038609589.1 1.5e-06 19_[+1]_31 cds-WP_051952161.1-2 1.6e-06 43_[+1]_7 rpsI 1.6e-06 1_[+1]_49 cds-WP_038611103.1 2e-06 [+1]_50 cds-WP_034999811.1 2.4e-06 33_[+1]_17 rplP 2.4e-06 10_[+1]_40 cds-WP_038610183.1-2 2.7e-06 22_[+1]_28 cds-WP_038610531.1 2.9e-06 5_[+1]_45 rpsK 3.5e-06 48_[+1]_2 nusB 5.6e-06 25_[+1]_25 cds-WP_038610359.1 7.3e-06 37_[+1]_13 rpsC 7.3e-06 43_[+1]_7 nusA 7.9e-06 17_[+1]_33 atpA 8.7e-06 13_[+1]_37 cds-WP_038610879.1 8.7e-06 12_[+1]_38 rpmC 9.4e-06 40_[+1]_10 cds-WP_038612278.1 1.1e-05 46_[+1]_4 cds-WP_144242416.1 1.6e-05 9_[+1]_41 cds-WP_038611949.1 2e-05 3_[+1]_47 rplW 2.9e-05 12_[+1]_38 rpsQ 3.2e-05 13_[+1]_37 rpsS 3.2e-05 32_[+1]_18 cds-WP_038614247.1 3.4e-05 32_[+1]_18 rpmA 4.6e-05 7_[+1]_43 cds-WP_038614395.1 6.6e-05 [+1]_50 cds-WP_038609252.1 6.6e-05 15_[+1]_35 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CSDCRMGVBCVBCGWCNHSVTSRNSVHSRTCSMSSDYGHSRHSDHSBMGM MEME-1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF CSDCRMGVBCVBCGWCNHSVTSRNSVHSRTCSMSSDYGHSRHSDHSBMGM width=50 seqs=48 rplB ( 10) CCGCGAGGGCAGCGACTCCATCGACATCTTCGGGGGTGCGACGGCCTAAC 1 rplQ ( 6) CGCCGAGACCGGGGACTATGTCGACACCAGCGCGGACGAGACCGAGTAAC 1 rplC ( 17) GCTCATGCGCATCGACCTGCCGGCCAGCGTCGACGTGAACATCCAGTAGA 1 rplO ( 45) CCTCAAGGTGCGCCACCTCGTCACCGTTGAAGAAGTTGCAGGGGAGTAGA 1 cds-WP_038611094.1 ( 4) CGTTGAGGCGCTCGCCCTCATCGGCCTCGTTGCCGGCTTCCTGTTCTAAA 1 rplE ( 33) CGGCTACCGCTTCGACGAGGACGGCAAGAAGGTCCGCGTGGCCAAGTCGA 1 rplD ( 11) CAACAACCTCATCCTGATCAAGGGCGCCATCCCGGGTGCCAAGGGTTCCG 1 cds-WP_038610255.1 ( 38) CAGCGGCAGCAGCTACGTCATGGGCAAGGCCGAAGACACCACAGATTCGG 1 rplV ( 7) CGATGAGTCCATGGTCGGCCACAAGCTCGGCGAGTTTGCACCGACCAAGA 1 cds-WP_038609175.1 ( 7) CGGCGTGGCCACTTGCGTGCTGCTCGCCTGCGTTGAGGCGGCGGAGGCGA 1 cds-WP_038611461.1 ( 4) CGTGGCGTGGACCGGCCTTGACGTGGACCCGGCCGTTGTCGCGGCCTCGA 1 cds-WP_038611097.1 ( 35) CCGCTCGAACACGATCGACGAGTTCCTAAGCGAGCTCGACCACGTGTCGA 1 cds-WP_038611109.1 ( 29) CTTCAACGGCCTTGGCGGTCTGGACGATGTCGAGGCTGCGTACAAGAAGC 1 cds-WP_038612979.1 ( 32) CACCGTGCGCCTCGACGACGTCGACGCCATGGCCGAGTTCCTTGCCCAGC 1 rpsG ( 6) CTACAAGATCATCCGCGGCGCGCTGGATACCCAGGGTGTGAAGGACCGCA 1 cds-WP_236627210.1 ( 49) CCTGTGGCTGATTGACCCTGTCTACGCCGACAAGGACGGGAAGTAGCCCA 1 cds-WP_038610255.1-2 ( 29) GGTGGGCTTCATCTTCTTTCTCGTCCCTTACAACATTGCGATGTATGGGA 1 rpsN ( 28) CCTGGCGTAGTGCAACTTCTTCATGCTGGGCCAACACGCGTTCGTGCAGC 1 rplS ( 36) CGGCTCGCGGGGCGTCCCCTTCACGGCGGTCCCAGGAGACAGGCTTGTGC 1 cds-WP_038611327.1 ( 19) CGTTGCCGTCGGTCTCCGGATGGGCCCCGTCAATTGAGCGAAAGTGTTGA 1 rplX ( 49) CGACAAGCGCTTCATGAAGATCGTGTCTCTCGCACCGGAGGTGATCTAAC 1 cds-WP_084768154.1 ( 20) CCGCGACGGCTTGGACCTGTAGCTCCCCCTCTTCGAGGTGGCGCCCGTAA 1 cds-WP_038609589.1 ( 20) CCAGGTAGCCGTCGTCAAGCACTTGCTTTACGACGGCACGACGAACGAAC 1 cds-WP_051952161.1-2 ( 44) CTTCATTTCCACCGTTGTTGTCATCCCCGACCCCTTAGACACCTACCCCC 1 rpsI ( 2) CCGTCAGTCCATCAAGAAGCTGCACGTCTTCGTCGGTGCCGAGCACCCGT 1 cds-WP_038611103.1 ( 1) CGACTCGAGCACCGTCGGCAAGAACCAGCTCAAAGTCAGCCGCTCCTAGT 1 cds-WP_034999811.1 ( 34) CCCCACTATCTGTCACTTGCTCACCCGCATCCCGCGGGAGAGCGCCTAGA 1 rplP ( 11) GAGCGCGGTGGCCGTGGCGACCGTGACCGTCGTCCGCGCCGCGGCGGCCA 1 cds-WP_038610183.1-2 ( 23) CGACAACGTCCGCGACACCGCCCGCAAACGCGGCGTCGCCCTCCCGGACC 1 cds-WP_038610531.1 ( 6) CGCCATGGTCCACCTCCCGGAGGACGCGATCCACGTTCGCCCCGGCGACA 1 rpsK ( 49) GCGCACCCGCAAGGGCCCGAAGAAGACCATCGCAGGAAAGAAGAAGTAAC 1 nusB ( 26) CGACAAGAACCTCTGCCCGTTGCACCAGTTCCACCTGTGGGCGTGGCCGC 1 cds-WP_038610359.1 ( 38) CGATGAGCGGGCCGTCGCCGAGAGCCATGTGGAGTACTCCTCAAGGTTGG 1 rpsC ( 44) CCGGAAGCGCACCTCCCACATCACCGTTGTTGTCGAGTCCAAGGAAGGGG 1 nusA ( 18) CGCGGCGACCGTCGTCTTTGCGACGACCGCCTGGCACGTAAACTTCTAGA 1 atpA ( 14) CGATGAGGTCATCGACGGTTCGACGCGCGGCAAACTTGACCGCCTTCGGA 1 cds-WP_038610879.1 ( 13) CCGAGCGCTCAGCATCGCCCACGCGAATCTCGTCCATCACAGCTCCCAAC 1 rpmC ( 41) CCGCGCTGGCGCGAAGCTGCCCTGCAAGGTCCGCGTGATCAAGAAGGAGG 1 cds-WP_038612278.1 ( 47) CTGTGAGGACGCGCACAACCTGGACCCCGGCGGCTGCCCGTCTATGTTGA 1 cds-WP_144242416.1 ( 10) GCGCATGTGGCGTTACTCTATCGCGCAGTACCGCTATGCCACACTTCCGC 1 cds-WP_038611949.1 ( 4) CTGGTTTCGGGGTTTGTCTGTGGACGCGATCCAGTATGACACAGATGTAG 1 rplW ( 13) GGTTGAGGCGCTGCACACCTTCATCAACCGCGGCAATGTCGTGGCTGCAG 1 rpsQ ( 14) CGACATCGCGCGCATCTACACGGTGCTGCGCGAGCGCGAGCTTGGCCTGT 1 rpsS ( 33) CCGTTATTCCAACAACATGATCGTGCGGCGCCGCCGCTCGAAGAAGCGCT 1 cds-WP_038614247.1 ( 33) CTGCACGAGCCGCTGGCCGATCGTCGCAATACGCCCCGCCGCGTCGGCCC 1 rpmA ( 8) GTTCTGGCCGATGTTCCAGGCGGTCCCAGTGGCGGTCGTCGTCTGGTGGC 1 cds-WP_038614395.1 ( 1) CGTCACCGGCGGCACCACCGCCTGGGTGGAACAAGGCTTGCCCCACCAAA 1 cds-WP_038609252.1 ( 16) CGAGGATGGCTGGGAGCTCGTCGCCGTCACGCCTGGTCCGACGCAAGACA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CSDCRMGVBCVBCGWCNHSVTSRNSVHSRTCSMSSDYGHSRHSDHSBMGM MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 50 n= 9333 bayes= 8.04517 E= 3.4e-007 -1223 152 -103 -1223 -134 16 56 -41 24 -151 33 48 -334 102 -67 -5 75 -383 62 -22 105 -3 -183 -5 -334 -38 107 -63 -17 -14 33 -22 -134 -25 49 37 -1223 129 -13 -1223 98 -38 -38 -63 -175 -51 16 103 -1223 112 -51 -41 -17 -84 62 -5 98 -225 -103 95 -1223 145 -84 -322 -17 16 -3 -5 12 7 -125 78 -1223 56 25 10 47 -38 25 -63 24 -51 -1223 148 -1223 92 56 -1223 36 -125 75 -90 36 -51 -67 78 -1223 116 16 -1223 24 41 16 -322 36 41 -183 37 -134 62 -13 -5 24 -67 49 -41 -34 -151 -38 137 -175 137 -125 -222 -102 7 87 -222 98 -25 -67 -41 -17 62 -3 -163 -234 -14 87 -41 47 -225 25 59 -134 41 -67 78 -76 -184 112 -41 24 56 -183 24 -175 75 56 -1223 112 -51 -25 -122 24 49 -125 10 -102 16 75 -163 -2 -67 41 10 98 -25 -125 10 -234 33 49 -22 -234 -14 -3 103 105 -3 -125 -41 12 -51 92 -1223 105 16 -103 -122 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CSDCRMGVBCVBCGWCNHSVTSRNSVHSRTCSMSSDYGHSRHSDHSBMGM MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 50 nsites= 48 E= 3.4e-007 0.000000 0.854167 0.145833 0.000000 0.083333 0.333333 0.437500 0.145833 0.250000 0.104167 0.375000 0.270833 0.020833 0.604167 0.187500 0.187500 0.354167 0.020833 0.458333 0.166667 0.437500 0.291667 0.083333 0.187500 0.020833 0.229167 0.625000 0.125000 0.187500 0.270833 0.375000 0.166667 0.083333 0.250000 0.416667 0.250000 0.000000 0.729167 0.270833 0.000000 0.416667 0.229167 0.229167 0.125000 0.062500 0.208333 0.333333 0.395833 0.000000 0.645833 0.208333 0.145833 0.187500 0.166667 0.458333 0.187500 0.416667 0.062500 0.145833 0.375000 0.000000 0.812500 0.166667 0.020833 0.187500 0.333333 0.291667 0.187500 0.229167 0.312500 0.125000 0.333333 0.000000 0.437500 0.354167 0.208333 0.291667 0.229167 0.354167 0.125000 0.250000 0.208333 0.000000 0.541667 0.000000 0.562500 0.437500 0.000000 0.270833 0.125000 0.500000 0.104167 0.270833 0.208333 0.187500 0.333333 0.000000 0.666667 0.333333 0.000000 0.250000 0.395833 0.333333 0.020833 0.270833 0.395833 0.083333 0.250000 0.083333 0.458333 0.270833 0.187500 0.250000 0.187500 0.416667 0.145833 0.166667 0.104167 0.229167 0.500000 0.062500 0.770833 0.125000 0.041667 0.104167 0.312500 0.541667 0.041667 0.416667 0.250000 0.187500 0.145833 0.187500 0.458333 0.291667 0.062500 0.041667 0.270833 0.541667 0.145833 0.291667 0.062500 0.354167 0.291667 0.083333 0.395833 0.187500 0.333333 0.125000 0.083333 0.645833 0.145833 0.250000 0.437500 0.083333 0.229167 0.062500 0.500000 0.437500 0.000000 0.458333 0.208333 0.250000 0.083333 0.250000 0.416667 0.125000 0.208333 0.104167 0.333333 0.500000 0.062500 0.208333 0.187500 0.395833 0.208333 0.416667 0.250000 0.125000 0.208333 0.041667 0.375000 0.416667 0.166667 0.041667 0.270833 0.291667 0.395833 0.437500 0.291667 0.125000 0.145833 0.229167 0.208333 0.562500 0.000000 0.437500 0.333333 0.145833 0.083333 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CSDCRMGVBCVBCGWCNHSVTSRNSVHSRTCSMSSDYGHSRHSDHSBMGM MEME-1 regular expression -------------------------------------------------------------------------------- C[GC][GTA]C[GA][AC][GC][GC][GCT][CG][ACG][TGC][CG]G[AT]C[CG][TCA][CGT][GAC][TAC][CG][GA][TAC][CG][CGA][CAT][CG][GA][TG]C[GC][AC][CG][GC][GAT][CT]G[CAT][CG][AGC][CAT][GC][GAT][ACT][GC][TGC][AC][GAC][AC] -------------------------------------------------------------------------------- Time 16.66 secs. ******************************************************************************** ******************************************************************************** MOTIF TGCTGGTTTAGTTCCTGTGCTTYAGACATGCTGTCGAGTTTGCA MEME-2 width = 44 sites = 2 llr = 124 E-value = 1.8e-002 ******************************************************************************** -------------------------------------------------------------------------------- Motif TGCTGGTTTAGTTCCTGTGCTTYAGACATGCTGTCGAGTTTGCA MEME-2 Description -------------------------------------------------------------------------------- Simplified A :::::::::a:::::::::::::a:a:a::::::::a::::::a pos.-specific C ::a::::::::::aa::::a::5:::a:::a:::a:::::::a: probability G :a::aa::::a:::::a:a:::::a::::a::a::a:a:::a:: matrix T a::a::aaa::aa::a:a::aa5:::::a::a:a::::aaa::: bits 2.4 * * *** ** * * ** * * * *** 2.1 * * **** ** * * ** * * ** * * * *** * 1.9 * * **** ** * * ** * * ** * * * *** * 1.7 ********************** ********************* Relative 1.4 ********************** ********************* Entropy 1.2 ********************** ********************* (89.7 bits) 0.9 ******************************************** 0.7 ******************************************** 0.5 ******************************************** 0.2 ******************************************** 0.0 -------------------------------------------- Multilevel TGCTGGTTTAGTTCCTGTGCTTCAGACATGCTGTCGAGTTTGCA consensus T sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TGCTGGTTTAGTTCCTGTGCTTYAGACATGCTGTCGAGTTTGCA MEME-2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------------------------------------------- cds-WP_144242426.1 1 3.92e-28 . TGCTGGTTTAGTTCCTGTGCTTTAGACATGCTGTCGAGTTTGCA CCCTCCAACT cds-WP_236627161.1 14 9.93e-28 GCCGATGAAT TGCTGGTTTAGTTCCTGTGCTTCAGACATGCTGTCGAGTTTGCA CCCCCAACTG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TGCTGGTTTAGTTCCTGTGCTTYAGACATGCTGTCGAGTTTGCA MEME-2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- cds-WP_144242426.1 3.9e-28 [+2]_56 cds-WP_236627161.1 9.9e-28 13_[+2]_43 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TGCTGGTTTAGTTCCTGTGCTTYAGACATGCTGTCGAGTTTGCA MEME-2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF TGCTGGTTTAGTTCCTGTGCTTYAGACATGCTGTCGAGTTTGCA width=44 seqs=2 cds-WP_144242426.1 ( 1) TGCTGGTTTAGTTCCTGTGCTTTAGACATGCTGTCGAGTTTGCA 1 cds-WP_236627161.1 ( 14) TGCTGGTTTAGTTCCTGTGCTTCAGACATGCTGTCGAGTTTGCA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TGCTGGTTTAGTTCCTGTGCTTYAGACATGCTGTCGAGTTTGCA MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 44 n= 10431 bayes= 12.3483 E= 1.8e-002 -765 -765 -765 236 -765 -765 174 -765 -765 174 -765 -765 -765 -765 -765 236 -765 -765 174 -765 -765 -765 174 -765 -765 -765 -765 236 -765 -765 -765 236 -765 -765 -765 236 224 -765 -765 -765 -765 -765 174 -765 -765 -765 -765 236 -765 -765 -765 236 -765 174 -765 -765 -765 174 -765 -765 -765 -765 -765 236 -765 -765 174 -765 -765 -765 -765 236 -765 -765 174 -765 -765 174 -765 -765 -765 -765 -765 236 -765 -765 -765 236 -765 75 -765 136 224 -765 -765 -765 -765 -765 174 -765 224 -765 -765 -765 -765 174 -765 -765 224 -765 -765 -765 -765 -765 -765 236 -765 -765 174 -765 -765 174 -765 -765 -765 -765 -765 236 -765 -765 174 -765 -765 -765 -765 236 -765 174 -765 -765 -765 -765 174 -765 224 -765 -765 -765 -765 -765 174 -765 -765 -765 -765 236 -765 -765 -765 236 -765 -765 -765 236 -765 -765 174 -765 -765 174 -765 -765 224 -765 -765 -765 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TGCTGGTTTAGTTCCTGTGCTTYAGACATGCTGTCGAGTTTGCA MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 44 nsites= 2 E= 1.8e-002 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.500000 0.000000 0.500000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TGCTGGTTTAGTTCCTGTGCTTYAGACATGCTGTCGAGTTTGCA MEME-2 regular expression -------------------------------------------------------------------------------- TGCTGGTTTAGTTCCTGTGCTT[CT]AGACATGCTGTCGAGTTTGCA -------------------------------------------------------------------------------- Time 30.22 secs. ******************************************************************************** ******************************************************************************** MOTIF CCAWCTGGTAGRTTHHAAGTGHCDGHTBCMTGCAVTTTCT MEME-3 width = 40 sites = 4 llr = 147 E-value = 1.2e+000 ******************************************************************************** -------------------------------------------------------------------------------- Motif CCAWCTGGTAGRTTHHAAGTGHCDGHTBCMTGCAVTTTCT MEME-3 Description -------------------------------------------------------------------------------- Simplified A ::85::::38:5::338a3::3:5333::5:3:a33:::: pos.-specific C a83:a::::33:::55:::3:5a::3:3a53:8:3:::83 probability G ::::::a8::853:::3:8:a::38::5:::8::5:3::: matrix T :3:5:a:38:::8a33:::8:3:3:583::8:3::88a38 bits 2.4 * * * 2.1 * * * * * 1.9 * * * * * 1.7 * *** * * * * * * * Relative 1.4 * ***** ** ** ** ** * * * * * *** * Entropy 1.2 ********** ** ** ** * * * * ** ***** (53.1 bits) 0.9 ************** ***** * * * ****** ***** 0.7 ************** ***** ***** ****** ***** 0.5 **************************************** 0.2 **************************************** 0.0 ---------------------------------------- Multilevel CCAACTGGTAGATTCCAAGTGCCAGTTGCATGCAGTTTCT consensus TCT TACCGG AAG AC A GAAAC CCAT AAG TC sequence TT T T C T C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCAWCTGGTAGRTTHHAAGTGHCDGHTBCMTGCAVTTTCT MEME-3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------------------------------- cds-WP_144242426.1 49 1.04e-23 TTTGCACCCT CCAACTGGTAGATTCCAAGTGCCAGTTTCATGCAATTTCT TTGGACCAGT cds-WP_236627161.1 61 2.13e-21 GTTTGCACCC CCAACTGGTAGATTCCAAGTGCCAGTTCCATATAGTTTCT infA 37 9.91e-16 CGCGCATGCG CCATCTGTACCGGTAAAAACGTCTGCTGCCTGCACTTTTT CAGGCGGCGT lexA 26 2.48e-15 CATGAGTGCC CTCTCTGGTAGGTTTTGAGTGACGAAAGCCCGCAGAGTCC CCTCACCAGA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCAWCTGGTAGRTTHHAAGTGHCDGHTBCMTGCAVTTTCT MEME-3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- cds-WP_144242426.1 1e-23 48_[+3]_12 cds-WP_236627161.1 2.1e-21 60_[+3] infA 9.9e-16 36_[+3]_24 lexA 2.5e-15 25_[+3]_35 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCAWCTGGTAGRTTHHAAGTGHCDGHTBCMTGCAVTTTCT MEME-3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF CCAWCTGGTAGRTTHHAAGTGHCDGHTBCMTGCAVTTTCT width=40 seqs=4 cds-WP_144242426.1 ( 49) CCAACTGGTAGATTCCAAGTGCCAGTTTCATGCAATTTCT 1 cds-WP_236627161.1 ( 61) CCAACTGGTAGATTCCAAGTGCCAGTTCCATATAGTTTCT 1 infA ( 37) CCATCTGTACCGGTAAAAACGTCTGCTGCCTGCACTTTTT 1 lexA ( 26) CTCTCTGGTAGGTTTTGAGTGACGAAAGCCCGCAGAGTCC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCAWCTGGTAGRTTHHAAGTGHCDGHTBCMTGCAVTTTCT MEME-3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 40 n= 11163 bayes= 12.1831 E= 1.2e+000 -865 175 -865 -865 -865 133 -865 36 183 -25 -865 -865 124 -865 -865 136 -865 175 -865 -865 -865 -865 -865 236 -865 -865 175 -865 -865 -865 133 36 24 -865 -865 195 183 -25 -865 -865 -865 -25 133 -865 124 -865 75 -865 -865 -865 -25 195 -865 -865 -865 236 24 75 -865 36 24 75 -865 36 183 -865 -25 -865 224 -865 -865 -865 24 -865 133 -865 -865 -25 -865 195 -865 -865 175 -865 24 75 -865 36 -865 175 -865 -865 124 -865 -25 36 24 -865 133 -865 24 -25 -865 136 24 -865 -865 195 -865 -25 75 36 -865 175 -865 -865 124 75 -865 -865 -865 -25 -865 195 24 -865 133 -865 -865 133 -865 36 224 -865 -865 -865 24 -25 75 -865 24 -865 -865 195 -865 -865 -25 195 -865 -865 -865 236 -865 133 -865 36 -865 -25 -865 195 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCAWCTGGTAGRTTHHAAGTGHCDGHTBCMTGCAVTTTCT MEME-3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 40 nsites= 4 E= 1.2e+000 0.000000 1.000000 0.000000 0.000000 0.000000 0.750000 0.000000 0.250000 0.750000 0.250000 0.000000 0.000000 0.500000 0.000000 0.000000 0.500000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.750000 0.250000 0.250000 0.000000 0.000000 0.750000 0.750000 0.250000 0.000000 0.000000 0.000000 0.250000 0.750000 0.000000 0.500000 0.000000 0.500000 0.000000 0.000000 0.000000 0.250000 0.750000 0.000000 0.000000 0.000000 1.000000 0.250000 0.500000 0.000000 0.250000 0.250000 0.500000 0.000000 0.250000 0.750000 0.000000 0.250000 0.000000 1.000000 0.000000 0.000000 0.000000 0.250000 0.000000 0.750000 0.000000 0.000000 0.250000 0.000000 0.750000 0.000000 0.000000 1.000000 0.000000 0.250000 0.500000 0.000000 0.250000 0.000000 1.000000 0.000000 0.000000 0.500000 0.000000 0.250000 0.250000 0.250000 0.000000 0.750000 0.000000 0.250000 0.250000 0.000000 0.500000 0.250000 0.000000 0.000000 0.750000 0.000000 0.250000 0.500000 0.250000 0.000000 1.000000 0.000000 0.000000 0.500000 0.500000 0.000000 0.000000 0.000000 0.250000 0.000000 0.750000 0.250000 0.000000 0.750000 0.000000 0.000000 0.750000 0.000000 0.250000 1.000000 0.000000 0.000000 0.000000 0.250000 0.250000 0.500000 0.000000 0.250000 0.000000 0.000000 0.750000 0.000000 0.000000 0.250000 0.750000 0.000000 0.000000 0.000000 1.000000 0.000000 0.750000 0.000000 0.250000 0.000000 0.250000 0.000000 0.750000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCAWCTGGTAGRTTHHAAGTGHCDGHTBCMTGCAVTTTCT MEME-3 regular expression -------------------------------------------------------------------------------- C[CT][AC][AT]CTG[GT][TA][AC][GC][AG][TG]T[CAT][CAT][AG]A[GA][TC]G[CAT]C[AGT][GA][TAC][TA][GCT]C[AC][TC][GA][CT]A[GAC][TA][TG]T[CT][TC] -------------------------------------------------------------------------------- Time 43.74 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- dnaN 7.62e-01 100 cds-WP_038608981.1 5.46e-01 100 cds-WP_051952093.1 3.02e-01 100 cds-WP_038609051.1 3.35e-01 100 cds-WP_038609173.1 8.00e-01 100 cds-WP_038609175.1 5.30e-04 6_[+1(2.74e-07)]_44 cds-WP_038609209.1 5.77e-01 100 cds-WP_038609252.1 6.84e-02 15_[+1(6.64e-05)]_35 cds-WP_038609318.1 1.57e-01 100 cds-WP_201773347.1 9.52e-01 100 cds-WP_038609473.1 5.82e-01 100 cds-WP_038609482.1 2.36e-01 100 cds-WP_070475253.1 2.34e-01 100 cds-WP_038609525.1 9.26e-01 100 cds-WP_038609549.1 3.53e-01 100 nusG 9.59e-01 100 rplK 7.63e-01 100 rplA 9.96e-01 100 rplJ 9.50e-01 100 rplL 5.57e-01 100 cds-WP_038609586.1 1.43e-01 100 cds-WP_038609589.1 2.60e-03 19_[+1(1.48e-06)]_31 rpsL 3.95e-01 100 rpsG 1.96e-04 5_[+1(6.54e-07)]_45 fusA 9.82e-01 100 tuf 1.20e-01 100 rpsJ 2.27e-01 100 rplC 2.14e-06 16_[+1(1.32e-09)]_34 rplD 2.24e-05 10_[+1(1.74e-07)]_40 rplW 1.55e-02 12_[+1(2.95e-05)]_38 rplB 2.86e-10 9_[+1(3.27e-14)]_41 rpsS 1.76e-02 32_[+1(3.18e-05)]_18 rplV 3.63e-07 6_[+1(2.45e-07)]_44 rpsC 7.10e-03 43_[+1(7.27e-06)]_7 rplP 3.58e-03 10_[+1(2.42e-06)]_40 rpmC 8.60e-03 40_[+1(9.44e-06)]_10 rpsQ 2.97e-02 13_[+1(3.18e-05)]_37 rplN 4.34e-02 100 rplX 8.99e-05 48_[+1(1.34e-06)]_2 rplE 1.43e-04 32_[+1(4.12e-08)]_18 rpsH 3.64e-01 100 rplF 5.07e-01 100 rplR 4.17e-02 100 rpsE 9.26e-01 100 rpmD 1.78e-01 100 rplO 2.67e-06 44_[+1(8.54e-09)]_6 infA 1.12e-11 36_[+3(9.91e-16)]_24 rpsM 3.59e-01 100 rpsK 2.02e-03 48_[+1(3.53e-06)]_2 rpsD 6.32e-01 100 cds-WP_038609724.1 2.36e-01 100 rplQ 9.10e-07 5_[+1(2.76e-10)]_45 rplM 4.75e-01 100 rpsI 1.13e-03 1_[+1(1.64e-06)]_49 cds-WP_038609794.1 4.85e-01 100 cds-WP_051952129.1 9.35e-02 100 cds-WP_051952132.1 4.96e-01 100 cds-WP_038609828.1 9.52e-01 100 cds-WP_038609850.1 4.05e-01 100 cds-WP_038609897.1 9.83e-02 100 cds-WP_038609911.1 5.53e-01 100 cds-WP_038609974.1 3.10e-01 100 cds-WP_038609977.1 6.67e-01 100 cds-WP_051952377.1 1.44e-01 100 cds-WP_038610090.1 6.08e-01 100 cds-WP_051952161.1 2.91e-01 100 cds-WP_038610183.1 3.11e-01 100 cds-WP_038610255.1 6.89e-04 37_[+1(2.45e-07)]_13 cds-WP_051952175.1 2.88e-01 100 cds-WP_038610359.1 3.96e-03 37_[+1(7.27e-06)]_13 cds-WP_038610377.1 3.40e-01 100 cds-WP_038610483.1 8.75e-01 100 rpsR 8.26e-01 100 rpsN 6.31e-04 27_[+1(8.06e-07)]_23 rpmG 8.13e-01 100 rpmB 7.24e-01 100 cds-WP_034999480.1 8.29e-02 100 cds-WP_038610531.1 2.47e-03 5_[+1(2.93e-06)]_45 cds-WP_084768153.1 8.25e-01 100 cds-WP_084768154.1 1.96e-03 19_[+1(1.48e-06)]_31 cds-WP_038610687.1 3.93e-01 100 cds-WP_051952190.1 1.29e-01 100 mfd 9.63e-01 100 greA 6.06e-01 100 cds-WP_051952193.1 1.41e-01 100 ychF 2.98e-01 100 cds-WP_034666346.1 3.48e-01 100 cds-WP_004601215.1 6.25e-01 100 cds-WP_005290994.1 2.99e-01 100 cds-WP_038610879.1 1.22e-03 12_[+1(8.66e-06)]_38 cds-WP_051952203.1 9.68e-01 100 sigE 9.89e-01 100 cds-WP_038611038.1 9.67e-02 100 cds-WP_051952212.1 6.89e-01 100 cds-WP_038611046.1 5.58e-01 100 rho 6.80e-01 100 cds-WP_038611081.1 2.41e-01 100 atpB 7.03e-01 100 cds-WP_034999811.1 1.17e-03 33_[+1(2.42e-06)]_17 cds-WP_038611094.1 4.10e-06 3_[+1(3.63e-08)]_47 cds-WP_038611097.1 4.68e-06 34_[+1(3.82e-07)]_16 atpA 6.95e-03 13_[+1(8.66e-06)]_37 cds-WP_038611103.1 4.34e-03 [+1(1.99e-06)]_50 atpD 6.75e-01 100 cds-WP_038611109.1 3.53e-05 28_[+1(4.26e-07)]_22 cds-WP_038611166.1 8.57e-01 100 cds-WP_069202889.1 6.59e-01 100 cds-WP_144242416.1 1.03e-02 9_[+1(1.56e-05)]_41 cds-WP_038611277.1 9.89e-01 100 cds-WP_038611327.1 2.04e-04 18_[+1(1.34e-06)]_32 cds-WP_038611336.1 2.89e-01 100 polA 4.81e-01 100 rpsA 9.19e-02 100 infC 2.73e-01 100 rpmI 8.28e-01 100 rplT 7.54e-01 100 cds-WP_038611461.1 3.17e-04 3_[+1(3.82e-07)]_47 cds-WP_051952230.1 7.69e-01 100 cds-WP_038611481.1 2.39e-01 100 cds-WP_038611542.1 2.78e-02 100 cds-WP_038611544.1 7.14e-01 100 cds-WP_144242426.1 8.35e-44 [+2(3.92e-28)]_4_[+3(1.04e-23)]_12 cds-WP_236627161.1 2.50e-41 13_[+2(9.93e-28)]_3_[+3(2.13e-21)] cds-WP_038611639.1 1.31e-01 100 cds-WP_051952243.1 4.79e-02 100 rpoZ 2.62e-01 100 nusB 9.96e-04 25_[+1(5.57e-06)]_25 efp 1.20e-01 100 ppgK 1.23e-01 100 cds-WP_038611916.1 1.82e-01 100 cds-WP_038611925.1 4.24e-01 100 cds-WP_038611927.1 2.49e-01 100 cds-WP_038611949.1 7.65e-04 3_[+1(1.99e-05)]_47 nrdR 1.12e-02 100 lexA 6.35e-11 25_[+3(2.48e-15)]_35 cds-WP_038611961.1 6.96e-01 100 cds-WP_051952258.1 3.19e-01 100 rpsO 6.06e-01 100 infB 5.45e-01 100 cds-WP_038612104.1 8.00e-01 100 nusA 3.77e-04 17_[+1(7.94e-06)]_33 tsf 3.22e-01 100 rpsB 3.26e-02 100 rplS 4.85e-05 35_[+1(1.21e-06)]_15 cds-WP_038612197.1 3.74e-01 100 rpsP 3.39e-01 100 cds-WP_038612278.1 1.16e-05 6_[+3(3.16e-05)]_[+1(1.12e-05)]_4 cds-WP_038612284.1 1.89e-01 100 dnaE 7.32e-01 100 cds-WP_038612328.1 6.16e-01 100 cds-WP_038614247.1 3.53e-02 32_[+1(3.43e-05)]_18 cds-WP_051952295.1 5.60e-01 100 hrcA 2.98e-02 100 rpsT 6.36e-01 100 holA 3.73e-01 100 rpmA 9.20e-03 7_[+1(4.63e-05)]_43 rplU 6.74e-01 100 cds-WP_051952305.1 6.22e-01 100 cds-WP_038612873.1 3.04e-01 100 ykgO 8.50e-01 100 cds-WP_201773330.1 9.13e-01 100 cds-WP_038612979.1 3.84e-04 31_[+1(5.29e-07)]_19 cds-WP_038612998.1 7.04e-01 100 cds-WP_038614395.1 5.05e-02 [+1(6.64e-05)]_50 cds-WP_051952332.1 3.16e-01 100 cds-WP_038613260.1 8.09e-01 100 cds-WP_038613274.1 5.09e-01 100 cds-WP_084768332.1 1.40e-01 100 cds-WP_038613314.1 1.76e-01 100 cds-WP_038613354.1 7.02e-02 100 cds-WP_051952347.1 1.88e-01 100 cds-WP_038613381.1 9.60e-01 100 cds-WP_038613390.1 9.35e-01 100 cds-WP_236627210.1 1.03e-04 48_[+1(7.26e-07)]_2 rplI 5.70e-01 100 rpsF 7.21e-01 100 cds-WP_038613525.1 1.58e-01 100 cds-WP_051952429.1 1.88e-01 100 cds-WP_038613532.1 2.13e-01 100 cds-WP_038613537.1 3.55e-01 100 cds-WP_051952161.1-2 4.01e-05 43_[+1(1.64e-06)]_7 cds-WP_038610183.1-2 3.60e-03 22_[+1(2.66e-06)]_28 cds-WP_038610255.1-2 6.46e-06 28_[+1(8.06e-07)]_22 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (3) found. ******************************************************************************** CPU: kodomo ********************************************************************************