******************************************************************************** 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 ------------- ------ ------ ------------- ------ ------ cds-WP_141406430.1 1.0000 100 mfd 1.0000 100 cds-WP_141406446.1 1.0000 100 cds-WP_010613905.1 1.0000 100 cds-WP_003787454.1 1.0000 100 cds-WP_141406464.1 1.0000 100 cds-WP_141406496.1 1.0000 100 cds-WP_141406517.1 1.0000 100 cds-WP_141406535.1 1.0000 100 cds-WP_141406541.1 1.0000 100 cds-WP_003780589.1 1.0000 100 cds-WP_141406555.1 1.0000 100 cds-WP_232622524.1 1.0000 100 cds-WP_081379346.1 1.0000 100 cds-WP_232622530.1 1.0000 100 rpmG 1.0000 100 cds-WP_020991756.1 1.0000 100 cds-WP_075378541.1 1.0000 100 cds-WP_003787091.1 1.0000 100 rplJ 1.0000 100 rplL 1.0000 100 rpoB 1.0000 100 cds-WP_009407052.1 1.0000 100 cds-WP_141406693.1 1.0000 100 cds-WP_010613374.1 1.0000 100 rho 1.0000 100 rpmE 1.0000 100 cds-WP_141406715.1 1.0000 100 cds-WP_141406718.1 1.0000 100 cds-WP_141406763.1 1.0000 100 cds-WP_003786636.1 1.0000 100 cds-WP_141406770.1 1.0000 100 cds-WP_141406782.1 1.0000 100 cds-WP_141406792.1 1.0000 100 rpsP 1.0000 100 rplS 1.0000 100 rpsB 1.0000 100 tsf 1.0000 100 nusA 1.0000 100 cds-WP_141406327.1 1.0000 100 infB 1.0000 100 rpsO 1.0000 100 dinB 1.0000 100 dnaE 1.0000 100 cds-WP_075378305.1 1.0000 100 infC 1.0000 100 rpmI 1.0000 100 rplT 1.0000 100 cds-WP_141406292.1 1.0000 100 cds-WP_141406290.1 1.0000 100 cds-WP_141406287.1 1.0000 100 cds-WP_141406278.1 1.0000 100 cds-WP_141406828.1 1.0000 100 cds-WP_009747484.1 1.0000 100 cds-WP_141406835.1 1.0000 100 cds-WP_075379005.1 1.0000 100 cds-WP_141406863.1 1.0000 100 cds-WP_141406864.1 1.0000 100 cds-WP_141406867.1 1.0000 100 cds-WP_232622568.1 1.0000 100 cds-WP_009233135.1 1.0000 100 cds-WP_232622573.1 1.0000 100 cds-WP_075379040.1 1.0000 100 cds-WP_141406923.1 1.0000 100 cds-WP_141406932.1 1.0000 100 cds-WP_075374311.1 1.0000 100 rpsD 1.0000 100 efp 1.0000 100 nusB 1.0000 100 rpoZ 1.0000 100 cds-WP_198498153.1 1.0000 100 cds-WP_141406959.1 1.0000 100 cds-WP_075379547.1 1.0000 100 cds-WP_009397704.1 1.0000 100 cds-WP_170198631.1 1.0000 100 scpB 1.0000 100 cds-WP_141406978.1 1.0000 100 rpsA 1.0000 100 polA 1.0000 100 cds-WP_075379321.1 1.0000 100 cds-WP_141407001.1 1.0000 100 cds-WP_141407006.1 1.0000 100 cds-WP_141407011.1 1.0000 100 cds-WP_141407186.1 1.0000 100 cds-WP_075378132.1 1.0000 100 cds-WP_232622602.1 1.0000 100 cds-WP_020991564.1 1.0000 100 cds-WP_141407053.1 1.0000 100 cds-WP_141407057.1 1.0000 100 hrcA 1.0000 100 rpsT 1.0000 100 cds-WP_232622604.1 1.0000 100 cds-WP_141407084.1 1.0000 100 cds-WP_070512522.1 1.0000 100 cds-WP_141407093.1 1.0000 100 rpmA 1.0000 100 rplU 1.0000 100 cds-WP_141407110.1 1.0000 100 rpmB 1.0000 100 cds-WP_004565203.1 1.0000 100 nrdR 1.0000 100 lexA 1.0000 100 cds-WP_004565236.1 1.0000 100 cds-WP_141407152.1 1.0000 100 cds-WP_141407161.1 1.0000 100 cds-WP_141407163.1 1.0000 100 cds-WP_198498092.1 1.0000 100 cds-WP_198498093.1 1.0000 100 cds-WP_141407433.1 1.0000 100 cds-WP_141407437.1 1.0000 100 cds-WP_141407400.1 1.0000 100 cds-WP_075377737.1 1.0000 100 cds-WP_070511825.1 1.0000 100 cds-WP_232622405.1 1.0000 100 rpmB_2 1.0000 100 rpmG_2 1.0000 100 rpsN 1.0000 100 cds-WP_141407359.1 1.0000 100 ykgO 1.0000 100 cds-WP_141407353.1 1.0000 100 atpD 1.0000 100 cds-WP_070661188.1 1.0000 100 atpA 1.0000 100 cds-WP_003789535.1 1.0000 100 cds-WP_020991854.1 1.0000 100 atpE 1.0000 100 atpB 1.0000 100 cds-WP_040321533.1 1.0000 100 cds-WP_141407351.1 1.0000 100 cds-WP_075379471.1 1.0000 100 cds-WP_141407334.1 1.0000 100 cds-WP_141406368.1 1.0000 100 cds-WP_141406383.1 1.0000 100 rpsI 1.0000 100 rplM 1.0000 100 cds-WP_075375122.1 1.0000 100 rplQ 1.0000 100 cds-WP_003789324.1 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_003781856.1 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 rplA 1.0000 100 rplK 1.0000 100 nusG 1.0000 100 cds-WP_141407451.1 1.0000 100 cds-WP_075378838.1 1.0000 100 cds-WP_003789164.1 1.0000 100 cds-WP_198498108.1 1.0000 100 ychF 1.0000 100 cds-WP_141407275.1 1.0000 100 cds-WP_075377942.1 1.0000 100 cds-WP_010614388.1 1.0000 100 cds-WP_075379148.1 1.0000 100 cds-WP_141407230.1 1.0000 100 cds-WP_070510430.1 1.0000 100 cds-WP_003779424.1 1.0000 100 cds-WP_141405746.1 1.0000 100 cds-WP_003787881.1 1.0000 100 cds-WP_101558972.1 1.0000 100 cds-WP_141405783.1 1.0000 100 cds-WP_141405784.1 1.0000 100 cds-WP_141405787.1 1.0000 100 cds-WP_269781166.1 1.0000 100 cds-WP_075378001.1 1.0000 100 cds-WP_070510020.1 1.0000 100 cds-WP_141405810.1 1.0000 100 cds-WP_170198561.1 1.0000 100 cds-WP_141405832.1 1.0000 100 cds-WP_141405857.1 1.0000 100 cds-WP_075378762.1 1.0000 100 cds-WP_070511153.1 1.0000 100 cds-WP_232622469.1 1.0000 100 cds-WP_141405905.1 1.0000 100 rplI 1.0000 100 rpsR 1.0000 100 rpsF 1.0000 100 cds-WP_141405924.1 1.0000 100 cds-WP_075250239.1 1.0000 100 dnaN 1.0000 100 cds-WP_141405941.1 1.0000 100 cds-WP_075414300.1 1.0000 100 cds-WP_141405948.1 1.0000 100 cds-WP_141405987.1 1.0000 100 cds-WP_141405994.1 1.0000 100 cds-WP_141406002.1 1.0000 100 cds-WP_141406024.1 1.0000 100 cds-WP_070510191.1 1.0000 100 cds-WP_141406041.1 1.0000 100 cds-WP_075373700.1 1.0000 100 cds-WP_075372097.1 1.0000 100 cds-WP_008732099.1 1.0000 100 cds-WP_141406118.1 1.0000 100 cds-WP_003788897.1 1.0000 100 cds-WP_141406131.1 1.0000 100 cds-WP_075414517.1 1.0000 100 cds-WP_010613285.1 1.0000 100 cds-WP_003788968.1 1.0000 100 cds-WP_141406196.1 1.0000 100 cds-WP_009407650.1 1.0000 100 cds-WP_141406223.1 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 -mod zoops -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= 22600 N= 226 sample: seed= 0 hsfrac= 0 searchsize= 22600 norand= no csites= 1000 Letter frequencies in dataset: A 0.176 C 0.314 G 0.325 T 0.185 Background letter frequencies (from file dataset with add-one prior applied): A 0.176 C 0.314 G 0.325 T 0.185 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF AGYKSBGGCDSCNGSNSKNSSRGNNGCTSSWSYKGSASNVG MEME-1 width = 41 sites = 46 llr = 537 E-value = 6.2e-015 ******************************************************************************** -------------------------------------------------------------------------------- Motif AGYKSBGGCDSCNGSNSKNSSRGNNGCTSSWSYKGSASNVG MEME-1 Description -------------------------------------------------------------------------------- Simplified A 5:11:12::5:23:132:3:13:221:11:3:22:25:331 pos.-specific C 135163226:56223342345223319145165134:5342 probability G 17:444572341385243263473381253:4137425227 matrix T 2:35:21:22123:23:42:21132::6:26:24::2:2:1 bits 2.5 2.3 2.0 1.8 Relative 1.5 Entropy 1.3 * (16.8 bits) 1.0 * * 0.8 * * * * * * *** * ** 0.5 ***** **** * * * **** ** * ** 0.3 ***** ******* ** * ** ************* ** 0.0 ----------------------------------------- Multilevel AGCTCGGGCACCTGGTGTAGCGGGGGCTGCTCCTGCACCCG consensus TCTGGCAC GG GCCACGCCGA CC CGAGTGCGGGAA sequence T T A C T TA T TG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AGYKSBGGCDSCNGSNSKNSSRGNNGCTSSWSYKGSASNVG MEME-1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ----------------------------------------- cds-WP_141405924.1 38 8.17e-11 CGGAAGCGGT AGCGCGCGCAGAAGCCGGACTGGTAGCTCCTCTAGAAGAAG GGGCTACTGC cds-WP_070661188.1 47 2.26e-09 CTCGGGCTCC TCCTCGGGCGGCGGCTCTCCTGGTGGCTCGTCGAGCACCAG TTCTCCCCGA cds-WP_020991854.1 52 4.09e-09 CGCCCGTACC AGCTCCGGGACCGGGAATAGCCGAAGCAGTACGGCGAGCAG CAGTTCAC rplW 10 1.27e-08 GGCTGGTCG AGTTGTGGATGCTGCAGGAGTTCAGGCTGCTGCAGCAGAAG TGCCGGAGAC cds-WP_232622604.1 48 2.48e-08 GTCCGGGTCG ACCGCGGCTAGCAGGAGTAGGCGCGGCCGCTCCTCCAGGAG CGGCTGGCTC atpE 2 4.71e-08 G AGAGGTAGCTCCGGGTGATCTGGTGGCTGGACAGGGACTCC GAGAAGTGCT rplQ 27 5.33e-08 CAGAGCCTGC TGCTGATGCGGTTGGGGTGCAAGTCGCTGCTCTGGGTCCGG ACTCGGCCGA rplC 4 7.72e-08 ACT AGCTGTAGCAGCTGGGCTGCGGGTTCCGGCAGCTGAGCGAG TACGCAGAGC cds-WP_141407353.1 15 1.25e-07 TAGCCACCGT AGCTCCTGGAGCTCGCAGCGCGGCGGCTCGAGTTGCGGACT CAGCAATCCT cds-WP_141407011.1 58 1.40e-07 GCGTTGCGGC AGCTGTGGCGGCTGGGCTGGAGGGTGGGCGTCCTCCACCGG CC cds-WP_003789535.1 10 1.57e-07 GCCGGGACA GGCTCGCCCAGTAGCTGGCGAAGGAGCTGCTCGAGCTCTGG TACCTCGGCC cds-WP_141405784.1 11 2.49e-07 GGCCCCTCAT TCCGCGGGCGGCTCGACGACGAGCAGCTCCTCACCGGGAGG CGCGCACCTC cds-WP_141406223.1 17 2.78e-07 GGCCGCCATC GGTTCCTCCGTCCGTCCTCGCGGTCGCTGTCCCTGCACTAG GCTGGGCAGC rplI 21 3.11e-07 GTCGCGTTCT AGCGGTTCCGGCACTTCTTGCGGGCGCTCTACCGAGACGAC GGGATGAGCT rplO 59 3.87e-07 GCGCCGGACT AACGGTGCCACGTGGTGGACCAGTGGCAACTCCTCCAGACT C rplP 18 4.80e-07 CCAAGCGCAG TCTTGTGGCTCGTCGTCGTCCGGCGGCTCGTCTGCGGCCGG CGGCTCTGGC cds-WP_081379346.1 6 7.31e-07 GGGCG AGCTCGAGCTGGAGGCCTCGCCCGGACTGCAGCTCTACTCC TTCACCTTCG rplR 31 8.10e-07 GGCCTCGGGA TGTTCCCGTTCCCGCACGCGATGCGGCCGCTCTTGCACGCG GCGTTCCAGC cds-WP_141407084.1 37 8.97e-07 TGCCGCCGCT ACATGGACCACCACCAAGAGTGGTAGCAGTAGCGAAAGCCG CCGGTCGACC cds-WP_141406118.1 55 9.93e-07 AGAGCGAGGG ACCGGCGCCTCTTGTCGCACGACGCGCTCCTCTGGCTCCCC GAGCA rpsI 8 1.48e-06 GTGGGCG TGCGGAGGGTCTCGGGCTTCTGCAAGCTCTAGTGGGTCCAG CGGGTCATTC rplB 37 1.63e-06 CAGTGGGACG CGCTCCCCTGGTAGCTGTAGAAGCCACTACACCGGATCACG CGGTGCCTTC rpmJ 3 1.63e-06 GG CCCACCAGCACCTCGACTCGGGGATGCTGGACAGGGCGCCG GCTTAGCAGA rpsE 20 1.80e-06 GTGCCGGCAC AGCGCCGGCAGCGGCTCCCGCGGGCACTCCCGCCGGACTTC GACACTCGTG cds-WP_141405746.1 22 1.98e-06 CGGGTGGTCC CCCACGAGGACCCGGACCTCCGGAAGCACCTCCGGCGGCGG GCGGCGTCGC cds-WP_003781856.1 17 2.39e-06 CCGTACCTGT AGTGGCACCACTGGTGCCGGTTCTGGCTGCTCCTCCGGGCG AGCGACGAGT rpsQ 28 2.88e-06 GCAGCGCTGT AGCGGGCGTAGATGTGCTAGCACGCGCTCGCACTCGAGCCA TAAGCGTGGC cds-WP_141406496.1 37 3.16e-06 CTCCAGTGGT TCTTCGCAGACCGGGTCGGGCAGATGCTCAAGGTGGAGAGG GAGATGCTGG fusA 12 3.46e-06 CTGTACGTGG CGTACCGGCTCAGGTTGTTCCGGAAGCGGGTGATGGCGACC ATCACGGCCT cds-WP_232622568.1 49 3.46e-06 TGGCCAGACG GGCTGGCGCAGCAGTGAGACCAGGTGCTGGCGTGCCGCGAC CAGGCGGCGC cds-WP_003789164.1 24 3.79e-06 CCCCCACCCA ACAGCAAGGACATGCTCGTGCATATCCTCCTCACGGAGTAT GTCGTGCGCG rpsC 37 3.79e-06 GAGTTCGCCT GGTCGGTGTAGTGGCAGTAGCAGCCCCTGTTCAGGCTGCGG CGTTGCTTCC cds-WP_075379321.1 1 3.79e-06 . ACGTCCGGTGCCGGCAATAGCGGCGGCAGTAGGAGGACCCA CGCCCGCAAT scpB 13 3.79e-06 CGGTACCCGC TCTAGTGGCACTGGACCACGCCGCCGGTCCTGCTGGACTGG CCGTACTACT cds-WP_003780589.1 31 4.53e-06 CACGAGGGCA AGCGCGCGCAGCGCGTGCGGCAGCCGCGACAACTGGACATT AGGTCAGCGG cds-WP_141406290.1 8 5.40e-06 TGCTAAG GGTTGCGGCTCAAGTCGTTGCGTTCGGTGGTGCCGTACTCC TGGTGGGGAA cds-WP_141406368.1 24 5.89e-06 GGCGGAGGCC TGCGCGGGCGCCGGCAGCCGGGCGAGGCGCACTGGCACCGG CGCATTGATG rplX 25 6.42e-06 TGCGCGTAGA AGCCGGGGCAGCCGGCACTCGAAGCACTCTTCTTCAAGTAC GCGTAGCAGA cds-WP_141407275.1 2 7.00e-06 C AGATCGACGTCCTGGTGGGGCTGGAGCGCTCCACGAGCAAG CGCAGCGTCT rpsN 13 7.00e-06 GTGACCCGCA AGAACCGCCGCAACACCCCCGACCGGCTGGTGCTGCGCAAG TTCGATCCGG atpD 32 7.62e-06 CTGCAGCAGC TCTTGGGGTGTGTCTGAGTGGAGTGGCTCGTCCTGGGGAGA GTCGAGACCT rplD 35 8.29e-06 GAGCAGTTGC CGCGCTAGGGGCCGGGGTTCCCGAGCCAGCAGCAGCAGGCG TGGCGGCACT cds-WP_009397704.1 15 9.78e-06 GCGTGGTCAA AGTCCACGCACAAGAAGGCCGCTGTCCTCGTCCAGCACTCG TACTTACTTC atpA 25 2.33e-05 TGGGTGTTGA AGTGGTGGGGTGGGGCGCGGCAGCAGCGAGTGCGGGTCGCG GCGGCCGGGG rpsS 1 2.70e-05 . CGTTCGGGCTCCCGGCGTGGGCGGCAGGGTTGTTCAGGTCG CTGGCGGAGT infA 6 3.36e-05 GCCCC TGGGCGGGCGCCACCCGGACGCGTTGCCGCTGGCGCTGACG GGCCGCCGCT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AGYKSBGGCDSCNGSNSKNSSRGNNGCTSSWSYKGSASNVG MEME-1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- cds-WP_141405924.1 8.2e-11 37_[+1]_22 cds-WP_070661188.1 2.3e-09 46_[+1]_13 cds-WP_020991854.1 4.1e-09 51_[+1]_8 rplW 1.3e-08 9_[+1]_50 cds-WP_232622604.1 2.5e-08 47_[+1]_12 atpE 4.7e-08 1_[+1]_58 rplQ 5.3e-08 26_[+1]_33 rplC 7.7e-08 3_[+1]_56 cds-WP_141407353.1 1.2e-07 14_[+1]_45 cds-WP_141407011.1 1.4e-07 57_[+1]_2 cds-WP_003789535.1 1.6e-07 9_[+1]_50 cds-WP_141405784.1 2.5e-07 10_[+1]_49 cds-WP_141406223.1 2.8e-07 16_[+1]_43 rplI 3.1e-07 20_[+1]_39 rplO 3.9e-07 58_[+1]_1 rplP 4.8e-07 17_[+1]_42 cds-WP_081379346.1 7.3e-07 5_[+1]_54 rplR 8.1e-07 30_[+1]_29 cds-WP_141407084.1 9e-07 36_[+1]_23 cds-WP_141406118.1 9.9e-07 54_[+1]_5 rpsI 1.5e-06 7_[+1]_52 rplB 1.6e-06 36_[+1]_23 rpmJ 1.6e-06 2_[+1]_57 rpsE 1.8e-06 19_[+1]_40 cds-WP_141405746.1 2e-06 21_[+1]_38 cds-WP_003781856.1 2.4e-06 16_[+1]_43 rpsQ 2.9e-06 27_[+1]_32 cds-WP_141406496.1 3.2e-06 36_[+1]_23 fusA 3.5e-06 11_[+1]_48 cds-WP_232622568.1 3.5e-06 48_[+1]_11 cds-WP_003789164.1 3.8e-06 23_[+1]_36 rpsC 3.8e-06 36_[+1]_23 cds-WP_075379321.1 3.8e-06 [+1]_59 scpB 3.8e-06 12_[+1]_47 cds-WP_003780589.1 4.5e-06 30_[+1]_29 cds-WP_141406290.1 5.4e-06 7_[+1]_52 cds-WP_141406368.1 5.9e-06 23_[+1]_36 rplX 6.4e-06 24_[+1]_35 cds-WP_141407275.1 7e-06 1_[+1]_58 rpsN 7e-06 12_[+1]_47 atpD 7.6e-06 31_[+1]_28 rplD 8.3e-06 34_[+1]_25 cds-WP_009397704.1 9.8e-06 14_[+1]_45 atpA 2.3e-05 24_[+1]_35 rpsS 2.7e-05 [+1]_59 infA 3.4e-05 5_[+1]_54 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AGYKSBGGCDSCNGSNSKNSSRGNNGCTSSWSYKGSASNVG MEME-1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF AGYKSBGGCDSCNGSNSKNSSRGNNGCTSSWSYKGSASNVG width=41 seqs=46 cds-WP_141405924.1 ( 38) AGCGCGCGCAGAAGCCGGACTGGTAGCTCCTCTAGAAGAAG 1 cds-WP_070661188.1 ( 47) TCCTCGGGCGGCGGCTCTCCTGGTGGCTCGTCGAGCACCAG 1 cds-WP_020991854.1 ( 52) AGCTCCGGGACCGGGAATAGCCGAAGCAGTACGGCGAGCAG 1 rplW ( 10) AGTTGTGGATGCTGCAGGAGTTCAGGCTGCTGCAGCAGAAG 1 cds-WP_232622604.1 ( 48) ACCGCGGCTAGCAGGAGTAGGCGCGGCCGCTCCTCCAGGAG 1 atpE ( 2) AGAGGTAGCTCCGGGTGATCTGGTGGCTGGACAGGGACTCC 1 rplQ ( 27) TGCTGATGCGGTTGGGGTGCAAGTCGCTGCTCTGGGTCCGG 1 rplC ( 4) AGCTGTAGCAGCTGGGCTGCGGGTTCCGGCAGCTGAGCGAG 1 cds-WP_141407353.1 ( 15) AGCTCCTGGAGCTCGCAGCGCGGCGGCTCGAGTTGCGGACT 1 cds-WP_141407011.1 ( 58) AGCTGTGGCGGCTGGGCTGGAGGGTGGGCGTCCTCCACCGG 1 cds-WP_003789535.1 ( 10) GGCTCGCCCAGTAGCTGGCGAAGGAGCTGCTCGAGCTCTGG 1 cds-WP_141405784.1 ( 11) TCCGCGGGCGGCTCGACGACGAGCAGCTCCTCACCGGGAGG 1 cds-WP_141406223.1 ( 17) GGTTCCTCCGTCCGTCCTCGCGGTCGCTGTCCCTGCACTAG 1 rplI ( 21) AGCGGTTCCGGCACTTCTTGCGGGCGCTCTACCGAGACGAC 1 rplO ( 59) AACGGTGCCACGTGGTGGACCAGTGGCAACTCCTCCAGACT 1 rplP ( 18) TCTTGTGGCTCGTCGTCGTCCGGCGGCTCGTCTGCGGCCGG 1 cds-WP_081379346.1 ( 6) AGCTCGAGCTGGAGGCCTCGCCCGGACTGCAGCTCTACTCC 1 rplR ( 31) TGTTCCCGTTCCCGCACGCGATGCGGCCGCTCTTGCACGCG 1 cds-WP_141407084.1 ( 37) ACATGGACCACCACCAAGAGTGGTAGCAGTAGCGAAAGCCG 1 cds-WP_141406118.1 ( 55) ACCGGCGCCTCTTGTCGCACGACGCGCTCCTCTGGCTCCCC 1 rpsI ( 8) TGCGGAGGGTCTCGGGCTTCTGCAAGCTCTAGTGGGTCCAG 1 rplB ( 37) CGCTCCCCTGGTAGCTGTAGAAGCCACTACACCGGATCACG 1 rpmJ ( 3) CCCACCAGCACCTCGACTCGGGGATGCTGGACAGGGCGCCG 1 rpsE ( 20) AGCGCCGGCAGCGGCTCCCGCGGGCACTCCCGCCGGACTTC 1 cds-WP_141405746.1 ( 22) CCCACGAGGACCCGGACCTCCGGAAGCACCTCCGGCGGCGG 1 cds-WP_003781856.1 ( 17) AGTGGCACCACTGGTGCCGGTTCTGGCTGCTCCTCCGGGCG 1 rpsQ ( 28) AGCGGGCGTAGATGTGCTAGCACGCGCTCGCACTCGAGCCA 1 cds-WP_141406496.1 ( 37) TCTTCGCAGACCGGGTCGGGCAGATGCTCAAGGTGGAGAGG 1 fusA ( 12) CGTACCGGCTCAGGTTGTTCCGGAAGCGGGTGATGGCGACC 1 cds-WP_232622568.1 ( 49) GGCTGGCGCAGCAGTGAGACCAGGTGCTGGCGTGCCGCGAC 1 cds-WP_003789164.1 ( 24) ACAGCAAGGACATGCTCGTGCATATCCTCCTCACGGAGTAT 1 rpsC ( 37) GGTCGGTGTAGTGGCAGTAGCAGCCCCTGTTCAGGCTGCGG 1 cds-WP_075379321.1 ( 1) ACGTCCGGTGCCGGCAATAGCGGCGGCAGTAGGAGGACCCA 1 scpB ( 13) TCTAGTGGCACTGGACCACGCCGCCGGTCCTGCTGGACTGG 1 cds-WP_003780589.1 ( 31) AGCGCGCGCAGCGCGTGCGGCAGCCGCGACAACTGGACATT 1 cds-WP_141406290.1 ( 8) GGTTGCGGCTCAAGTCGTTGCGTTCGGTGGTGCCGTACTCC 1 cds-WP_141406368.1 ( 24) TGCGCGGGCGCCGGCAGCCGGGCGAGGCGCACTGGCACCGG 1 rplX ( 25) AGCCGGGGCAGCCGGCACTCGAAGCACTCTTCTTCAAGTAC 1 cds-WP_141407275.1 ( 2) AGATCGACGTCCTGGTGGGGCTGGAGCGCTCCACGAGCAAG 1 rpsN ( 13) AGAACCGCCGCAACACCCCCGACCGGCTGGTGCTGCGCAAG 1 atpD ( 32) TCTTGGGGTGTGTCTGAGTGGAGTGGCTCGTCCTGGGGAGA 1 rplD ( 35) CGCGCTAGGGGCCGGGGTTCCCGAGCCAGCAGCAGCAGGCG 1 cds-WP_009397704.1 ( 15) AGTCCACGCACAAGAAGGCCGCTGTCCTCGTCCAGCACTCG 1 atpA ( 25) AGTGGTGGGGTGGGGCGCGGCAGCAGCGAGTGCGGGTCGCG 1 rpsS ( 1) CGTTCGGGCTCCCGGCGTGGGCGGCAGGGTTGTTCAGGTCG 1 infA ( 6) TGGGCGGGCGCCACCCGGACGCGTTGCCGCTGGCGCTGACG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AGYKSBGGCDSCNGSNSKNSSRGNNGCTSSWSYKGSASNVG MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 41 n= 13560 bayes= 9.2653 E= 6.2e-015 157 -127 -158 37 -302 -15 110 -1217 -70 79 -290 72 -70 -227 18 131 -1217 85 42 -1217 -102 -15 35 24 30 -68 56 -76 -302 -39 118 -1217 -302 100 -73 -28 137 -1217 -10 37 -1217 67 42 -150 -21 85 -158 -9 57 -105 -20 72 -1217 -53 127 -1217 -143 -15 49 8 57 -27 -73 61 -21 39 42 -1217 -202 -68 10 116 79 -27 -73 37 -1217 32 90 -1217 -70 61 -32 -28 98 -85 27 -109 -302 -85 118 -150 15 -27 -20 50 44 -15 -10 -9 -70 -153 127 -1217 -1217 150 -158 -1217 -43 -185 -109 177 -102 39 62 -1217 -302 54 -10 24 89 -153 -1217 161 -202 85 27 -1217 -21 61 -132 37 -21 -127 0 108 -202 -27 110 -1217 -21 39 27 -208 163 -285 -44 -9 -1217 79 49 -1217 68 -5 -90 37 79 39 -44 -208 -143 -68 100 -109 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AGYKSBGGCDSCNGSNSKNSSRGNNGCTSSWSYKGSASNVG MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 41 nsites= 46 E= 6.2e-015 0.521739 0.130435 0.108696 0.239130 0.021739 0.282609 0.695652 0.000000 0.108696 0.543478 0.043478 0.304348 0.108696 0.065217 0.369565 0.456522 0.000000 0.565217 0.434783 0.000000 0.086957 0.282609 0.413043 0.217391 0.217391 0.195652 0.478261 0.108696 0.021739 0.239130 0.739130 0.000000 0.021739 0.630435 0.195652 0.152174 0.456522 0.000000 0.304348 0.239130 0.000000 0.500000 0.434783 0.065217 0.152174 0.565217 0.108696 0.173913 0.260870 0.152174 0.282609 0.304348 0.000000 0.217391 0.782609 0.000000 0.065217 0.282609 0.456522 0.195652 0.260870 0.260870 0.195652 0.282609 0.152174 0.413043 0.434783 0.000000 0.043478 0.195652 0.347826 0.413043 0.304348 0.260870 0.195652 0.239130 0.000000 0.391304 0.608696 0.000000 0.108696 0.478261 0.260870 0.152174 0.347826 0.173913 0.391304 0.086957 0.021739 0.173913 0.739130 0.065217 0.195652 0.260870 0.282609 0.260870 0.239130 0.282609 0.304348 0.173913 0.108696 0.108696 0.782609 0.000000 0.000000 0.891304 0.108696 0.000000 0.130435 0.086957 0.152174 0.630435 0.086957 0.413043 0.500000 0.000000 0.021739 0.456522 0.304348 0.217391 0.326087 0.108696 0.000000 0.565217 0.043478 0.565217 0.391304 0.000000 0.152174 0.478261 0.130435 0.239130 0.152174 0.130435 0.326087 0.391304 0.043478 0.260870 0.695652 0.000000 0.152174 0.413043 0.391304 0.043478 0.543478 0.043478 0.239130 0.173913 0.000000 0.543478 0.456522 0.000000 0.282609 0.304348 0.173913 0.239130 0.304348 0.413043 0.239130 0.043478 0.065217 0.195652 0.652174 0.086957 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AGYKSBGGCDSCNGSNSKNSSRGNNGCTSSWSYKGSASNVG MEME-1 regular expression -------------------------------------------------------------------------------- [AT][GC][CT][TG][CG][GCT][GA][GC]C[AGT][CG]C[TGA][GC][GC][TAC][GC][TG][ACT][GC][CG][GA]G[GCT][GCA]GCT[GC][CGT][TA][CG][CT][TG][GC][CG][AG][CG][CAT][CAG]G -------------------------------------------------------------------------------- Time 23.14 secs. ******************************************************************************** ******************************************************************************** MOTIF KCDWGRAAKDGKRVGKTWVGASTWWVACRGRCVTRAMANAKYHABWWST MEME-2 width = 49 sites = 8 llr = 214 E-value = 6.9e+000 ******************************************************************************** -------------------------------------------------------------------------------- Motif KCDWGRAAKDGKRVGKTWVGASTWWVACRGRCVTRAMANAKYHABWWST MEME-2 Description -------------------------------------------------------------------------------- Simplified A 1154166614115331:43:61155361415:4:5956391139155:1 pos.-specific C :6:11::1:::1:4::3:5:14:::5161:18311:413:153:4::51 probability G 5:318431439443651:3815:1:33:493:4:3:1131411:31141 matrix T 4334::1154:4111466:31:945::31:13:911:13:434134416 bits 2.5 2.3 2.0 * * * 1.8 * * * * * Relative 1.5 * * * * * * * Entropy 1.3 * * * * * * * * * * (38.6 bits) 1.0 ** * * * *** * * * * * * * ** 0.8 *** ******* * **** ** *** ** * * * *** * * ** * 0.5 *********** * **** ** *** ** ********* * * ** * 0.3 ************* ************************ ***** **** 0.0 ------------------------------------------------- Multilevel GCAAGAAATAGGACGGTTCGAGTAACACAGACATAAAAAAGCTACAACT consensus TTGT GG GT TGAATCAAT C TTAGTG GTG G C C TTA GTTG sequence T G G G G C G C T T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif KCDWGRAAKDGKRVGKTWVGASTWWVACRGRCVTRAMANAKYHABWWST MEME-2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------------------------------------------- cds-WP_141406383.1 24 4.18e-19 CGCCTACGGT GATAAAAATTGTACGTTTGGAGTAACACAGACATAACAAACTAACTGCT GGTGTCACAC cds-WP_198498093.1 38 5.25e-13 CCTCGAGATC GCACGGATGAGGACGATTCGACATTCACCAGCGTAAATGAACCAAAAGT CGGACAATGG cds-WP_141406290.1 51 5.25e-13 CGTACTCCTG GTGGGGAATAGCAAGTGAAGACTTAGCAAGACATAACATGGCAACAAGA G cds-WP_003787881.1 42 7.91e-13 CGCCACCTGG TCGTGAACTGAGGGGGCACGTGTATGACAGATATCACACATACATGTCT TCCTCAACGG cds-WP_141406718.1 6 8.58e-13 GCAAG GCAAGAAGAGGTGGGGTTGGGCTGTAACTGTCGTATGACAGCTACAACT GTCGTACGAC cds-WP_141407433.1 7 1.28e-12 CCAGAG TCAACATAGAGTAAAGTACTCGTAAAACGGGCCTTAAGGATTTTGTTCC CCTAAGGCCC mfd 13 1.50e-12 GGGGTATAAT ATTTGAGAGTGATTTTCTCTAGTTTCGTGGACGCGAAAAAGGTATTAGT GCCCCGCTGC rpoZ 36 1.62e-12 CTGGAGAGAC TCATGGGATTGGGCAGTTAGAATAACGTGGCTCTGAACTATCGAGATTG AACCGGAGGC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif KCDWGRAAKDGKRVGKTWVGASTWWVACRGRCVTRAMANAKYHABWWST MEME-2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- cds-WP_141406383.1 4.2e-19 23_[+2]_28 cds-WP_198498093.1 5.3e-13 37_[+2]_14 cds-WP_141406290.1 5.3e-13 50_[+2]_1 cds-WP_003787881.1 7.9e-13 41_[+2]_10 cds-WP_141406718.1 8.6e-13 5_[+2]_46 cds-WP_141407433.1 1.3e-12 6_[+2]_45 mfd 1.5e-12 12_[+2]_39 rpoZ 1.6e-12 35_[+2]_16 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif KCDWGRAAKDGKRVGKTWVGASTWWVACRGRCVTRAMANAKYHABWWST MEME-2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF KCDWGRAAKDGKRVGKTWVGASTWWVACRGRCVTRAMANAKYHABWWST width=49 seqs=8 cds-WP_141406383.1 ( 24) GATAAAAATTGTACGTTTGGAGTAACACAGACATAACAAACTAACTGCT 1 cds-WP_198498093.1 ( 38) GCACGGATGAGGACGATTCGACATTCACCAGCGTAAATGAACCAAAAGT 1 cds-WP_141406290.1 ( 51) GTGGGGAATAGCAAGTGAAGACTTAGCAAGACATAACATGGCAACAAGA 1 cds-WP_003787881.1 ( 42) TCGTGAACTGAGGGGGCACGTGTATGACAGATATCACACATACATGTCT 1 cds-WP_141406718.1 ( 6) GCAAGAAGAGGTGGGGTTGGGCTGTAACTGTCGTATGACAGCTACAACT 1 cds-WP_141407433.1 ( 7) TCAACATAGAGTAAAGTACTCGTAAAACGGGCCTTAAGGATTTTGTTCC 1 mfd ( 13) ATTTGAGAGTGATTTTCTCTAGTTTCGTGGACGCGAAAAAGGTATTAGT 1 rpoZ ( 36) TCATGGGATTGGGCAGTTAGAATAACGTGGCTCTGAACTATCGAGATTG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif KCDWGRAAKDGKRVGKTWVGASTWWVACRGRCVTRAMANAKYHABWWST MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 49 n= 11752 bayes= 10.5196 E= 6.9e+000 -49 -965 62 102 -49 99 -965 44 150 -965 -38 44 109 -133 -138 102 -49 -133 120 -965 183 -965 21 -965 183 -965 -38 -56 183 -133 -138 -56 -49 -965 21 144 109 -965 -38 102 -49 -965 143 -965 -49 -133 21 102 150 -965 21 -56 51 25 -38 -56 51 -965 94 -56 -49 -965 62 102 -965 -33 -138 176 109 -965 -965 176 51 67 -38 -965 -965 -965 120 44 183 -133 -138 -56 -49 25 62 -965 -49 -965 -965 224 150 -965 -138 102 150 -965 -965 144 51 67 -38 -965 183 -133 -38 -965 -49 99 -965 44 109 -133 21 -56 -49 -965 143 -965 150 -133 -38 -56 -965 125 -965 44 109 -33 21 -965 -965 -133 -965 224 150 -133 -38 -56 231 -965 -965 -56 150 25 -138 -965 183 -133 -138 -56 51 -33 -38 44 231 -965 -138 -965 -49 -133 21 102 -49 67 -138 44 51 -33 -138 102 231 -965 -965 -56 -49 25 -38 44 150 -965 -138 102 150 -965 -138 102 -965 67 21 -56 -49 -133 -138 176 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif KCDWGRAAKDGKRVGKTWVGASTWWVACRGRCVTRAMANAKYHABWWST MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 49 nsites= 8 E= 6.9e+000 0.125000 0.000000 0.500000 0.375000 0.125000 0.625000 0.000000 0.250000 0.500000 0.000000 0.250000 0.250000 0.375000 0.125000 0.125000 0.375000 0.125000 0.125000 0.750000 0.000000 0.625000 0.000000 0.375000 0.000000 0.625000 0.000000 0.250000 0.125000 0.625000 0.125000 0.125000 0.125000 0.125000 0.000000 0.375000 0.500000 0.375000 0.000000 0.250000 0.375000 0.125000 0.000000 0.875000 0.000000 0.125000 0.125000 0.375000 0.375000 0.500000 0.000000 0.375000 0.125000 0.250000 0.375000 0.250000 0.125000 0.250000 0.000000 0.625000 0.125000 0.125000 0.000000 0.500000 0.375000 0.000000 0.250000 0.125000 0.625000 0.375000 0.000000 0.000000 0.625000 0.250000 0.500000 0.250000 0.000000 0.000000 0.000000 0.750000 0.250000 0.625000 0.125000 0.125000 0.125000 0.125000 0.375000 0.500000 0.000000 0.125000 0.000000 0.000000 0.875000 0.500000 0.000000 0.125000 0.375000 0.500000 0.000000 0.000000 0.500000 0.250000 0.500000 0.250000 0.000000 0.625000 0.125000 0.250000 0.000000 0.125000 0.625000 0.000000 0.250000 0.375000 0.125000 0.375000 0.125000 0.125000 0.000000 0.875000 0.000000 0.500000 0.125000 0.250000 0.125000 0.000000 0.750000 0.000000 0.250000 0.375000 0.250000 0.375000 0.000000 0.000000 0.125000 0.000000 0.875000 0.500000 0.125000 0.250000 0.125000 0.875000 0.000000 0.000000 0.125000 0.500000 0.375000 0.125000 0.000000 0.625000 0.125000 0.125000 0.125000 0.250000 0.250000 0.250000 0.250000 0.875000 0.000000 0.125000 0.000000 0.125000 0.125000 0.375000 0.375000 0.125000 0.500000 0.125000 0.250000 0.250000 0.250000 0.125000 0.375000 0.875000 0.000000 0.000000 0.125000 0.125000 0.375000 0.250000 0.250000 0.500000 0.000000 0.125000 0.375000 0.500000 0.000000 0.125000 0.375000 0.000000 0.500000 0.375000 0.125000 0.125000 0.125000 0.125000 0.625000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif KCDWGRAAKDGKRVGKTWVGASTWWVACRGRCVTRAMANAKYHABWWST MEME-2 regular expression -------------------------------------------------------------------------------- [GT][CT][AGT][AT]G[AG][AG]A[TG][ATG]G[GT][AG][CAG][GA][GT][TC][TA][CAG][GT]A[GC]T[AT][AT][CAG][AG][CT][AG]G[AG][CT][AGC]T[AG]A[AC]A[ACGT]A[GT][CT][TAC]A[CGT][AT][AT][CG]T -------------------------------------------------------------------------------- Time 44.18 secs. ******************************************************************************** ******************************************************************************** MOTIF WMAYVAGGAAGGAGA MEME-3 width = 15 sites = 17 llr = 195 E-value = 2.7e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif WMAYVAGGAAGGAGA MEME-3 Description -------------------------------------------------------------------------------- Simplified A 547:36216a:1a16 pos.-specific C :43643112::::12 probability G 12::41661:a9:82 matrix T 41:4::12::::::: bits 2.5 * * 2.3 * * 2.0 * * 1.8 * * Relative 1.5 * ** * Entropy 1.3 * * **** (16.5 bits) 1.0 * ** * ****** 0.8 * ** * ******* 0.5 * ** ** ******* 0.3 *************** 0.0 --------------- Multilevel ACACCAGGAAGGAGA consensus TACTGCA C C sequence A -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif WMAYVAGGAAGGAGA MEME-3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------- cds-WP_141406923.1 81 5.37e-08 GTGGAGCCAG TACTGAGGAAGGAGA CTACG ykgO 77 1.60e-07 CCCTCACTGG ACACGAAGAAGGAAA GGAGCCGAC cds-WP_010614388.1 80 3.78e-07 CGTCATCACG AACCAAGGAAGGAGG GTTCAC cds-WP_075378305.1 81 4.22e-07 ACGGGTGCCT TCACGAGTCAGGAGA AGCTC cds-WP_075377737.1 15 6.10e-07 CCACAGCCAG TACTCAGCAAGGAGA GGAGTCTAAT cds-WP_141406763.1 1 8.70e-07 . AGATGAGGGAGGAGA GCACGTCGTT cds-WP_141406446.1 81 9.70e-07 GGGCCCCGCC TCATCCGCAAGGAGA GCCAC rplL 79 1.20e-06 CGCAGGAACC TGATAAGGAAGGAAC GCCCATC rplJ 82 2.56e-06 CCCTGCGGCA TACCACGGAAGGAGG GCCC cds-WP_141407437.1 85 3.08e-06 TGTTTCCGAC ACACCAAGGAGGAGC C cds-WP_081379346.1 79 3.67e-06 GTGAGAGCGG ACATGACTCAGGAGA CGGTGCG cds-WP_003788968.1 79 5.14e-06 GCGGTAACCC ACCTCAAGCAGGAGC CCACCCC cds-WP_075250239.1 49 6.02e-06 CAGTCGCGAG ATACCCGGAAGAAGA AGCCACAGCC rpsB 83 6.02e-06 ACCTCTCGGC ACACACGGAAGGACC GTC rpmE 81 6.48e-06 CGGGACCCTC TGACGCTTAAGGAGA AACCT infB 83 7.01e-06 CCGGGGTGGG AAACCGGACAGGAGA AAA cds-WP_232622573.1 80 7.56e-06 AGCACGTAAG GAACAAAAAAGGAGG GACACT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif WMAYVAGGAAGGAGA MEME-3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- cds-WP_141406923.1 5.4e-08 80_[+3]_5 ykgO 1.6e-07 76_[+3]_9 cds-WP_010614388.1 3.8e-07 79_[+3]_6 cds-WP_075378305.1 4.2e-07 80_[+3]_5 cds-WP_075377737.1 6.1e-07 14_[+3]_71 cds-WP_141406763.1 8.7e-07 [+3]_85 cds-WP_141406446.1 9.7e-07 80_[+3]_5 rplL 1.2e-06 78_[+3]_7 rplJ 2.6e-06 81_[+3]_4 cds-WP_141407437.1 3.1e-06 84_[+3]_1 cds-WP_081379346.1 3.7e-06 78_[+3]_7 cds-WP_003788968.1 5.1e-06 78_[+3]_7 cds-WP_075250239.1 6e-06 48_[+3]_37 rpsB 6e-06 82_[+3]_3 rpmE 6.5e-06 80_[+3]_5 infB 7e-06 82_[+3]_3 cds-WP_232622573.1 7.6e-06 79_[+3]_6 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif WMAYVAGGAAGGAGA MEME-3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF WMAYVAGGAAGGAGA width=15 seqs=17 cds-WP_141406923.1 ( 81) TACTGAGGAAGGAGA 1 ykgO ( 77) ACACGAAGAAGGAAA 1 cds-WP_010614388.1 ( 80) AACCAAGGAAGGAGG 1 cds-WP_075378305.1 ( 81) TCACGAGTCAGGAGA 1 cds-WP_075377737.1 ( 15) TACTCAGCAAGGAGA 1 cds-WP_141406763.1 ( 1) AGATGAGGGAGGAGA 1 cds-WP_141406446.1 ( 81) TCATCCGCAAGGAGA 1 rplL ( 79) TGATAAGGAAGGAAC 1 rplJ ( 82) TACCACGGAAGGAGG 1 cds-WP_141407437.1 ( 85) ACACCAAGGAGGAGC 1 cds-WP_081379346.1 ( 79) ACATGACTCAGGAGA 1 cds-WP_003788968.1 ( 79) ACCTCAAGCAGGAGC 1 cds-WP_075250239.1 ( 49) ATACCCGGAAGAAGA 1 rpsB ( 83) ACACACGGAAGGACC 1 rpmE ( 81) TGACGCTTAAGGAGA 1 infB ( 83) AAACCGGACAGGAGA 1 cds-WP_232622573.1 ( 80) GAACAAAAAAGGAGG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif WMAYVAGGAAGGAGA MEME-3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 19436 bayes= 10.2273 E= 2.7e+001 159 -1073 -246 116 100 39 -88 -165 200 -10 -1073 -1073 -1073 90 -1073 116 74 17 12 -1073 188 -10 -246 -1073 42 -241 99 -165 -58 -142 86 -6 188 -42 -147 -1073 251 -1073 -1073 -1073 -1073 -1073 162 -1073 -158 -1073 153 -1073 251 -1073 -1073 -1073 -58 -241 134 -1073 174 -42 -88 -1073 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif WMAYVAGGAAGGAGA MEME-3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 17 E= 2.7e+001 0.529412 0.000000 0.058824 0.411765 0.352941 0.411765 0.176471 0.058824 0.705882 0.294118 0.000000 0.000000 0.000000 0.588235 0.000000 0.411765 0.294118 0.352941 0.352941 0.000000 0.647059 0.294118 0.058824 0.000000 0.235294 0.058824 0.647059 0.058824 0.117647 0.117647 0.588235 0.176471 0.647059 0.235294 0.117647 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.058824 0.000000 0.941176 0.000000 1.000000 0.000000 0.000000 0.000000 0.117647 0.058824 0.823529 0.000000 0.588235 0.235294 0.176471 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif WMAYVAGGAAGGAGA MEME-3 regular expression -------------------------------------------------------------------------------- [AT][CA][AC][CT][CGA][AC][GA]G[AC]AGGAG[AC] -------------------------------------------------------------------------------- Time 64.03 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- cds-WP_141406430.1 5.49e-01 100 mfd 1.94e-08 12_[+2(1.50e-12)]_39 cds-WP_141406446.1 7.19e-04 80_[+3(9.70e-07)]_5 cds-WP_010613905.1 8.43e-01 100 cds-WP_003787454.1 3.91e-01 100 cds-WP_141406464.1 3.48e-01 100 cds-WP_141406496.1 3.46e-04 36_[+1(3.16e-06)]_23 cds-WP_141406517.1 6.89e-01 100 cds-WP_141406535.1 8.49e-01 100 cds-WP_141406541.1 1.42e-02 33_[+3(5.47e-05)]_52 cds-WP_003780589.1 5.55e-04 30_[+1(4.53e-06)]_29 cds-WP_141406555.1 5.06e-01 100 cds-WP_232622524.1 1.30e-01 100 cds-WP_081379346.1 2.19e-06 5_[+1(7.31e-07)]_32_[+3(3.67e-06)]_\ 7 cds-WP_232622530.1 5.68e-01 100 rpmG 7.38e-01 100 cds-WP_020991756.1 4.71e-01 100 cds-WP_075378541.1 6.99e-01 100 cds-WP_003787091.1 6.70e-01 100 rplJ 7.78e-03 81_[+3(2.56e-06)]_4 rplL 2.05e-03 78_[+3(1.20e-06)]_7 rpoB 3.11e-01 100 cds-WP_009407052.1 4.59e-01 100 cds-WP_141406693.1 2.43e-01 100 cds-WP_010613374.1 4.29e-01 100 rho 8.96e-01 100 rpmE 1.25e-02 80_[+3(6.48e-06)]_5 cds-WP_141406715.1 3.59e-01 100 cds-WP_141406718.1 1.30e-08 5_[+2(8.58e-13)]_46 cds-WP_141406763.1 1.19e-04 [+3(8.70e-07)]_85 cds-WP_003786636.1 8.90e-02 100 cds-WP_141406770.1 3.73e-01 100 cds-WP_141406782.1 4.51e-01 100 cds-WP_141406792.1 7.32e-02 100 rpsP 4.53e-02 100 rplS 2.05e-01 100 rpsB 4.86e-03 82_[+3(6.02e-06)]_3 tsf 3.29e-01 100 nusA 3.43e-01 100 cds-WP_141406327.1 1.91e-01 100 infB 2.32e-03 82_[+3(7.01e-06)]_3 rpsO 8.84e-02 100 dinB 5.32e-01 100 dnaE 1.82e-01 100 cds-WP_075378305.1 1.11e-03 80_[+3(4.22e-07)]_5 infC 6.37e-01 100 rpmI 4.87e-01 100 rplT 1.75e-02 100 cds-WP_141406292.1 9.36e-01 100 cds-WP_141406290.1 2.44e-12 7_[+1(5.40e-06)]_2_[+2(5.25e-13)]_1 cds-WP_141406287.1 3.61e-01 100 cds-WP_141406278.1 8.84e-01 100 cds-WP_141406828.1 4.12e-01 100 cds-WP_009747484.1 5.15e-03 79_[+3(5.97e-05)]_6 cds-WP_141406835.1 8.67e-01 100 cds-WP_075379005.1 6.68e-01 100 cds-WP_141406863.1 2.66e-01 100 cds-WP_141406864.1 1.96e-01 100 cds-WP_141406867.1 5.42e-01 100 cds-WP_232622568.1 6.41e-03 48_[+1(3.46e-06)]_11 cds-WP_009233135.1 2.15e-01 100 cds-WP_232622573.1 1.07e-03 79_[+3(7.56e-06)]_6 cds-WP_075379040.1 5.28e-01 100 cds-WP_141406923.1 7.02e-06 80_[+3(5.37e-08)]_5 cds-WP_141406932.1 5.01e-01 100 cds-WP_075374311.1 9.72e-01 100 rpsD 8.00e-01 100 efp 2.15e-01 100 nusB 3.95e-01 100 rpoZ 1.39e-08 35_[+2(1.62e-12)]_16 cds-WP_198498153.1 6.53e-01 100 cds-WP_141406959.1 1.78e-01 100 cds-WP_075379547.1 1.38e-01 100 cds-WP_009397704.1 2.08e-03 14_[+1(9.78e-06)]_45 cds-WP_170198631.1 8.60e-01 100 scpB 6.59e-03 12_[+1(3.79e-06)]_47 cds-WP_141406978.1 4.40e-01 100 rpsA 5.47e-02 100 polA 7.22e-01 100 cds-WP_075379321.1 3.42e-03 [+1(3.79e-06)]_59 cds-WP_141407001.1 7.33e-01 100 cds-WP_141407006.1 1.48e-01 100 cds-WP_141407011.1 3.11e-04 57_[+1(1.40e-07)]_2 cds-WP_141407186.1 3.62e-01 100 cds-WP_075378132.1 2.76e-01 100 cds-WP_232622602.1 8.97e-01 100 cds-WP_020991564.1 2.15e-01 100 cds-WP_141407053.1 4.43e-01 100 cds-WP_141407057.1 8.46e-01 100 hrcA 3.62e-01 100 rpsT 1.91e-01 100 cds-WP_232622604.1 2.34e-05 47_[+1(2.48e-08)]_12 cds-WP_141407084.1 2.33e-03 36_[+1(8.97e-07)]_23 cds-WP_070512522.1 2.06e-01 100 cds-WP_141407093.1 2.07e-01 100 rpmA 1.91e-01 100 rplU 1.95e-01 100 cds-WP_141407110.1 8.83e-01 100 rpmB 4.50e-01 100 cds-WP_004565203.1 9.99e-01 100 nrdR 6.18e-01 100 lexA 3.90e-01 100 cds-WP_004565236.1 1.00e+00 100 cds-WP_141407152.1 2.98e-01 100 cds-WP_141407161.1 2.76e-01 100 cds-WP_141407163.1 1.37e-01 100 cds-WP_198498092.1 2.81e-01 100 cds-WP_198498093.1 3.30e-10 37_[+2(5.25e-13)]_14 cds-WP_141407433.1 6.93e-09 6_[+2(1.28e-12)]_45 cds-WP_141407437.1 1.46e-03 84_[+3(3.08e-06)]_1 cds-WP_141407400.1 4.20e-01 100 cds-WP_075377737.1 4.70e-05 14_[+3(6.10e-07)]_71 cds-WP_070511825.1 9.37e-01 100 cds-WP_232622405.1 8.96e-01 100 rpmB_2 1.86e-01 100 rpmG_2 2.88e-01 100 rpsN 3.35e-04 12_[+1(7.00e-06)]_47 cds-WP_141407359.1 3.14e-01 100 ykgO 2.45e-05 76_[+3(1.60e-07)]_9 cds-WP_141407353.1 5.41e-04 14_[+1(1.25e-07)]_45 atpD 8.70e-03 31_[+1(7.62e-06)]_28 cds-WP_070661188.1 1.40e-05 46_[+1(2.26e-09)]_13 atpA 1.35e-02 24_[+1(2.33e-05)]_35 cds-WP_003789535.1 7.13e-06 9_[+1(1.57e-07)]_50 cds-WP_020991854.1 5.55e-07 51_[+1(4.09e-09)]_8 atpE 9.33e-05 1_[+1(4.71e-08)]_58 atpB 6.72e-02 100 cds-WP_040321533.1 9.71e-02 100 cds-WP_141407351.1 8.41e-01 100 cds-WP_075379471.1 2.63e-01 100 cds-WP_141407334.1 9.84e-01 100 cds-WP_141406368.1 4.24e-03 23_[+1(5.89e-06)]_36 cds-WP_141406383.1 6.43e-15 23_[+2(4.18e-19)]_28 rpsI 2.77e-03 7_[+1(1.48e-06)]_52 rplM 4.79e-01 100 cds-WP_075375122.1 4.33e-02 [+3(7.31e-05)]_85 rplQ 8.78e-05 26_[+1(5.33e-08)]_33 cds-WP_003789324.1 4.80e-01 100 rpsK 8.66e-01 100 rpsM 2.30e-01 100 rpmJ 3.58e-03 2_[+1(1.63e-06)]_57 infA 3.69e-02 5_[+1(3.36e-05)]_54 rplO 8.77e-04 58_[+1(3.87e-07)]_1 rpmD 3.58e-01 100 rpsE 4.64e-03 19_[+1(1.80e-06)]_40 rplR 2.52e-03 30_[+1(8.10e-07)]_29 rplF 2.47e-01 100 rpsH 9.16e-01 100 cds-WP_003781856.1 4.28e-03 16_[+1(2.39e-06)]_43 rplE 3.04e-01 100 rplX 8.04e-03 24_[+1(6.42e-06)]_35 rplN 9.83e-01 100 rpsQ 2.91e-03 27_[+1(2.88e-06)]_32 rpmC 2.80e-01 100 rplP 1.68e-03 17_[+1(4.80e-07)]_42 rpsC 6.91e-03 36_[+1(3.79e-06)]_23 rplV 3.07e-01 100 rpsS 2.25e-03 [+1(2.70e-05)]_59 rplB 2.83e-03 36_[+1(1.63e-06)]_23 rplW 2.49e-07 9_[+1(1.27e-08)]_13_[+3(5.47e-05)]_\ 22 rplD 1.54e-03 34_[+1(8.29e-06)]_25 rplC 2.77e-05 3_[+1(7.72e-08)]_56 rpsJ 9.87e-01 100 tuf 8.32e-01 100 fusA 2.88e-03 11_[+1(3.46e-06)]_48 rpsG 4.35e-01 100 rpsL 7.91e-01 100 rplA 2.57e-01 100 rplK 7.83e-01 100 nusG 4.03e-01 100 cds-WP_141407451.1 1.60e-01 100 cds-WP_075378838.1 3.87e-01 100 cds-WP_003789164.1 2.14e-03 23_[+1(3.79e-06)]_36 cds-WP_198498108.1 8.11e-01 100 ychF 6.50e-01 100 cds-WP_141407275.1 6.68e-03 1_[+1(7.00e-06)]_58 cds-WP_075377942.1 8.69e-01 100 cds-WP_010614388.1 8.90e-04 79_[+3(3.78e-07)]_6 cds-WP_075379148.1 7.52e-01 100 cds-WP_141407230.1 6.04e-01 100 cds-WP_070510430.1 8.60e-01 100 cds-WP_003779424.1 7.78e-01 100 cds-WP_141405746.1 1.84e-04 21_[+1(1.98e-06)]_38 cds-WP_003787881.1 5.35e-09 41_[+2(7.91e-13)]_10 cds-WP_101558972.1 6.50e-01 100 cds-WP_141405783.1 2.60e-01 100 cds-WP_141405784.1 4.42e-04 10_[+1(2.49e-07)]_49 cds-WP_141405787.1 7.51e-01 100 cds-WP_269781166.1 5.09e-01 100 cds-WP_075378001.1 7.89e-01 100 cds-WP_070510020.1 9.06e-01 100 cds-WP_141405810.1 4.09e-01 100 cds-WP_170198561.1 5.67e-01 100 cds-WP_141405832.1 9.27e-01 100 cds-WP_141405857.1 3.45e-01 100 cds-WP_075378762.1 3.57e-01 100 cds-WP_070511153.1 8.71e-01 100 cds-WP_232622469.1 2.33e-01 100 cds-WP_141405905.1 8.06e-01 100 rplI 7.71e-04 20_[+1(3.11e-07)]_39 rpsR 3.24e-01 100 rpsF 3.59e-01 100 cds-WP_141405924.1 2.25e-08 37_[+1(8.17e-11)]_22 cds-WP_075250239.1 2.27e-03 48_[+3(6.02e-06)]_37 dnaN 5.15e-01 100 cds-WP_141405941.1 6.33e-02 100 cds-WP_075414300.1 7.79e-01 100 cds-WP_141405948.1 6.25e-01 100 cds-WP_141405987.1 3.04e-01 100 cds-WP_141405994.1 3.96e-01 100 cds-WP_141406002.1 5.29e-01 100 cds-WP_141406024.1 5.30e-01 100 cds-WP_070510191.1 6.84e-01 100 cds-WP_141406041.1 9.74e-01 100 cds-WP_075373700.1 8.89e-01 100 cds-WP_075372097.1 7.24e-01 100 cds-WP_008732099.1 4.44e-01 100 cds-WP_141406118.1 8.47e-04 54_[+1(9.93e-07)]_5 cds-WP_003788897.1 3.08e-01 100 cds-WP_141406131.1 2.78e-01 100 cds-WP_075414517.1 9.26e-01 100 cds-WP_010613285.1 1.02e-01 100 cds-WP_003788968.1 4.21e-03 78_[+3(5.14e-06)]_7 cds-WP_141406196.1 3.80e-01 100 cds-WP_009407650.1 5.94e-01 100 cds-WP_141406223.1 6.05e-04 16_[+1(2.78e-07)]_43 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (3) found. ******************************************************************************** CPU: kodomo ********************************************************************************