******************************************************************************** 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-NP_214537.1 1.0000 100 cds-NP_214552.1 1.0000 100 cds-NP_214556.1 1.0000 100 cds-NP_214557.1 1.0000 100 cds-NP_214561.1 1.0000 100 cds-NP_214566.3 1.0000 100 rpsF 1.0000 100 rpsR1 1.0000 100 rplI 1.0000 100 cds-NP_214581.1 1.0000 100 cds-NP_214592.1 1.0000 100 cds-NP_214595.1 1.0000 100 nrp 1.0000 100 rpmB1 1.0000 100 oxyS 1.0000 100 fusA2 1.0000 100 cds-NP_214649.1 1.0000 100 cds-NP_214658.1 1.0000 100 cds-NP_214672.1 1.0000 100 mce1R 1.0000 100 sigG 1.0000 100 cds-NP_214710.1 1.0000 100 cds-NP_214746.1 1.0000 100 cds-NP_214752.1 1.0000 100 cds-NP_214787.1 1.0000 100 cds-YP_177706.1 1.0000 100 cds-NP_214816.1 1.0000 100 cds-NP_214842.1 1.0000 100 cds-NP_214844.1 1.0000 100 cds-NP_214891.1 1.0000 100 sigK 1.0000 100 cds-NP_214979.1 1.0000 100 cds-NP_214986.1 1.0000 100 cds-NP_214988.1 1.0000 100 cds-NP_214999.1 1.0000 100 cds-NP_215008.2 1.0000 100 mce2R 1.0000 100 cds-YP_177629.1 1.0000 100 rpmG2 1.0000 100 nusG 1.0000 100 rplK 1.0000 100 rplA 1.0000 100 cds-NP_215164.1 1.0000 100 rplJ 1.0000 100 rplL 1.0000 100 cds-NP_215167.1 1.0000 100 vapB6 1.0000 100 mazE2 1.0000 100 rpoB 1.0000 100 rpoC 1.0000 100 lpqP 1.0000 100 cds-NP_215188.1 1.0000 100 rpsL 1.0000 100 rpsG 1.0000 100 fusA1 1.0000 100 tuf 1.0000 100 cds-NP_215205.1 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 rpsN1 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 cds-NP_215244.1 1.0000 100 sigL 1.0000 100 rslA 1.0000 100 cds-NP_215251.1 1.0000 100 cds-NP_215281.1 1.0000 100 cds-NP_215307.1 1.0000 100 cds-NP_215317.1 1.0000 100 cds-NP_215337.1 1.0000 100 kmtR 1.0000 100 cds-NP_215395.1 1.0000 100 rimJ 1.0000 100 rplY 1.0000 100 cds-NP_215535.1 1.0000 100 mfd 1.0000 100 cds-NP_215560.1 1.0000 100 cds-NP_215565.1 1.0000 100 greA 1.0000 100 cds-NP_215628.1 1.0000 100 cds-NP_215645.1 1.0000 100 cds-NP_215668.1 1.0000 100 cds-NP_215683.1 1.0000 100 cds-NP_215692.1 1.0000 100 sigI 1.0000 100 cds-NP_215735.1 1.0000 100 sigE 1.0000 100 relE 1.0000 100 cds-NP_215771.1 1.0000 100 embR 1.0000 100 cds-NP_215803.1 1.0000 100 rho 1.0000 100 rpmE 1.0000 100 cds-NP_215817.1 1.0000 100 atpB 1.0000 100 atpE 1.0000 100 atpF 1.0000 100 atpH 1.0000 100 atpA 1.0000 100 atpG 1.0000 100 atpD 1.0000 100 atpC 1.0000 100 rpoZ 1.0000 100 cds-NP_215920.1 1.0000 100 cds-NP_215976.2 1.0000 100 cds-NP_215990.1 1.0000 100 cds-NP_216021.1 1.0000 100 cds-NP_216050.1 1.0000 100 dinX 1.0000 100 dnaE1 1.0000 100 cds-NP_216072.1 1.0000 100 vapB11 1.0000 100 cds-NP_216095.1 1.0000 100 polA 1.0000 100 rpsA 1.0000 100 infC 1.0000 100 rpmI 1.0000 100 rplT 1.0000 100 cds-NP_216201.1 1.0000 100 scpB 1.0000 100 cds-NP_216235.1 1.0000 100 cds-NP_216241.1 1.0000 100 cds-NP_216289.1 1.0000 100 cds-NP_216344.1 1.0000 100 blaI 1.0000 100 cds-NP_216446.1 1.0000 100 cds-NP_216447.1 1.0000 100 parD1 1.0000 100 mce3R 1.0000 100 cds-NP_216501.1 1.0000 100 mazE6 1.0000 100 cmtR 1.0000 100 vapB15 1.0000 100 cds-NP_216537.1 1.0000 100 cds-NP_216550.1 1.0000 100 rpsR2 1.0000 100 rpsN2 1.0000 100 rpmG1 1.0000 100 rpmB2 1.0000 100 sigC 1.0000 100 pafC 1.0000 100 pafB 1.0000 100 cds-NP_216648.1 1.0000 100 cds-NP_216707.1 1.0000 100 cds-NP_216766.2 1.0000 100 cds-NP_216798.1 1.0000 100 cds-NP_216840.1 1.0000 100 cds-NP_216843.1 1.0000 100 smtB 1.0000 100 hrcA 1.0000 100 cds-NP_216891.1 1.0000 100 mbtF 1.0000 100 mbtE 1.0000 100 mbtB 1.0000 100 rpsT 1.0000 100 cds-NP_216929.3 1.0000 100 rpmA 1.0000 100 rplU 1.0000 100 cds-NP_217022.1 1.0000 100 vapB17 1.0000 100 nusB 1.0000 100 efp 1.0000 100 vapB18 1.0000 100 fadD9 1.0000 100 cds-NP_217134.1 1.0000 100 cds-NP_217137.1 1.0000 100 cds-NP_217156.1 1.0000 100 cds-NP_217158.1 1.0000 100 ppgK 1.0000 100 sigA 1.0000 100 cds-NP_217220.1 1.0000 100 sigB 1.0000 100 ideR 1.0000 100 nrdR 1.0000 100 lexA 1.0000 100 clgR 1.0000 100 vapB21 1.0000 100 cds-NP_217295.2 1.0000 100 rpsO 1.0000 100 sirR 1.0000 100 mazE9 1.0000 100 infB 1.0000 100 cds-NP_217356.3 1.0000 100 nusA 1.0000 100 relG 1.0000 100 cds-NP_217403.1 1.0000 100 tsf 1.0000 100 rpsB 1.0000 100 rplS 1.0000 100 rpsP 1.0000 100 cds-NP_217428.1 1.0000 100 tesA 1.0000 100 cds-YP_009030042.1 1.0000 100 cds-NP_217505.1 1.0000 100 cds-NP_217566.1 1.0000 100 cds-NP_217571.1 1.0000 100 dinP 1.0000 100 cds-NP_217574.1 1.0000 100 cds-NP_217576.1 1.0000 100 pknK 1.0000 100 cds-NP_217611.1 1.0000 100 moaR1 1.0000 100 cds-NP_217676.1 1.0000 100 cds-NP_217683.1 1.0000 100 cds-NP_217689.1 1.0000 100 cds-NP_217699.1 1.0000 100 cds-NP_217724.1 1.0000 100 sigH 1.0000 100 cds-NP_217766.1 1.0000 100 manB 1.0000 100 cds-NP_217784.1 1.0000 100 sigF 1.0000 100 lrpA 1.0000 100 cds-NP_217812.1 1.0000 100 lpqC 1.0000 100 sigJ 1.0000 100 cds-NP_217851.1 1.0000 100 dnaE2 1.0000 100 acrA1 1.0000 100 cds-NP_217911.1 1.0000 100 cds-NP_217922.1 1.0000 100 sigD 1.0000 100 rpsI 1.0000 100 rplM 1.0000 100 rplQ 1.0000 100 rpoA 1.0000 100 rpsD 1.0000 100 rpsK 1.0000 100 rpsM 1.0000 100 rpmJ 1.0000 100 infA 1.0000 100 cds-NP_218001.1 1.0000 100 cds-NP_218005.1 1.0000 100 cds-NP_218074.1 1.0000 100 kstR 1.0000 100 cds-NP_218092.1 1.0000 100 cds-NP_218100.1 1.0000 100 cds-NP_218117.1 1.0000 100 cds-NP_218161.1 1.0000 100 cds-NP_218192.1 1.0000 100 cds-NP_218195.1 1.0000 100 dnaQ 1.0000 100 dnaZX 1.0000 100 cds-NP_218239.2 1.0000 100 nmtR 1.0000 100 cds-NP_218305.1 1.0000 100 cds-NP_218347.1 1.0000 100 cds-NP_218350.1 1.0000 100 cds-NP_218357.1 1.0000 100 ethR 1.0000 100 pcnA 1.0000 100 sigM 1.0000 100 parB 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= 270 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= 27000 N= 270 sample: seed= 0 hsfrac= 0 searchsize= 27000 norand= no csites= 1000 Letter frequencies in dataset: A 0.199 C 0.305 G 0.306 T 0.191 Background letter frequencies (from file dataset with add-one prior applied): A 0.199 C 0.305 G 0.306 T 0.191 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF CRRCGACGAKGBVGWGSSMAGCGATGAGGAGVAGMDSSGC MEME-1 width = 40 sites = 7 llr = 217 E-value = 4.0e-010 ******************************************************************************** -------------------------------------------------------------------------------- Motif CRRCGACGAKGBVGWGSSMAGCGATGAGGAGVAGMDSSGC MEME-1 Description -------------------------------------------------------------------------------- Simplified A :43::711a:::4:6:::471::9::9:19:39:34:::: pos.-specific C 9:17::91:1:43:116361:a::1::1:1:3::6:363a probability G :661a3:7:3a33a:936::7:a:1a199:94:a:3647: matrix T 1::1:::::6:3::3:11:11::17:::::1:1:131::: bits 2.4 * 2.2 * 1.9 * 1.7 * * * * *** ** * ** * Relative 1.4 * * * * *** ** * ** * Entropy 1.2 * *** * * * * * *** ****** ** * (44.7 bits) 1.0 ** *** * * *** ** ********** ** ** 0.7 ** ******** *** ************* **** *** 0.5 *********** ******************* ******** 0.2 **************************************** 0.0 ---------------------------------------- Multilevel CGGCGACGATGCAGAGCGCAGCGATGAGGAGGAGCAGCGC consensus AA G G GC T GCA A AGCGC sequence TG C T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CRRCGACGAKGBVGWGSSMAGCGATGAGGAGVAGMDSSGC MEME-1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------------------------------- rplB 11 3.96e-22 CGGCCTAGCC CGGCGACGATGCAGAGCGAAGCGATGAGGAGGAGCAGGGC AATGCGGCCT cds-NP_215817.1 59 1.32e-21 TGACCCGCGC CAGCGACGATGCAGAGCGAAGCGATGAGGAGAAGCGGCGC CA scpB 59 2.14e-18 TTTCGTGGAC CGGTGACGATGCAGAGCGCAGCGATGAGAAGGAGCGGCGC TT rpsH 4 8.97e-15 GCG CAGCGGCGAGGGGGCCGCAAGCGATGAGGAGGAGTAGCGC TCGATGACCG atpG 7 4.16e-13 GGTGCC CGACGAACATGTCGAGGCCCTCGACGAGGATAAGCTCGCC AAGGAAGCCG rplW 17 1.25e-12 ACGTGCTGCG TGCCGACGACGTGGTGTTCAGCGTTGAGGCGCTGAATGCC TATATCGCGG rplR 32 3.29e-12 CCGATCCGTA CAAGGGCAAGGGCGTGCGCTACGAGGGCGAGCAGATCCGC CGCAAGGTCG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CRRCGACGAKGBVGWGSSMAGCGATGAGGAGVAGMDSSGC MEME-1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- rplB 4e-22 10_[+1]_50 cds-NP_215817.1 1.3e-21 58_[+1]_2 scpB 2.1e-18 58_[+1]_2 rpsH 9e-15 3_[+1]_57 atpG 4.2e-13 6_[+1]_54 rplW 1.2e-12 16_[+1]_44 rplR 3.3e-12 31_[+1]_29 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CRRCGACGAKGBVGWGSSMAGCGATGAGGAGVAGMDSSGC MEME-1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF CRRCGACGAKGBVGWGSSMAGCGATGAGGAGVAGMDSSGC width=40 seqs=7 rplB ( 11) CGGCGACGATGCAGAGCGAAGCGATGAGGAGGAGCAGGGC 1 cds-NP_215817.1 ( 59) CAGCGACGATGCAGAGCGAAGCGATGAGGAGAAGCGGCGC 1 scpB ( 59) CGGTGACGATGCAGAGCGCAGCGATGAGAAGGAGCGGCGC 1 rpsH ( 4) CAGCGGCGAGGGGGCCGCAAGCGATGAGGAGGAGTAGCGC 1 atpG ( 7) CGACGAACATGTCGAGGCCCTCGACGAGGATAAGCTCGCC 1 rplW ( 17) TGCCGACGACGTGGTGTTCAGCGTTGAGGCGCTGAATGCC 1 rplR ( 32) CAAGGGCAAGGGCGTGCGCTACGAGGGCGAGCAGATCCGC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CRRCGACGAKGBVGWGSSMAGCGATGAGGAGVAGMDSSGC MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 40 n= 16470 bayes= 11.0434 E= 4.0e-010 -945 149 -945 -41 110 -945 90 -945 52 -109 90 -945 -945 123 -110 -41 -945 -945 171 -945 184 -945 -10 -945 -48 149 -945 -945 -48 -109 122 -945 233 -945 -945 -945 -945 -109 -10 158 -945 -945 171 -945 -945 49 -10 58 110 -9 -10 -945 -945 -945 171 -945 152 -109 -945 58 -945 -109 149 -945 -945 91 -10 -41 -945 -9 90 -41 110 91 -945 -945 184 -109 -945 -41 -48 -945 122 -41 -945 171 -945 -945 -945 -945 171 -945 210 -945 -945 -41 -945 -109 -110 190 -945 -945 171 -945 210 -945 -110 -945 -945 -109 149 -945 -48 -945 149 -945 210 -109 -945 -945 -945 -945 149 -41 52 -9 49 -945 210 -945 -945 -41 -945 -945 171 -945 52 91 -945 -41 110 -945 -10 58 -945 -9 90 -41 -945 91 49 -945 -945 -9 122 -945 -945 171 -945 -945 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CRRCGACGAKGBVGWGSSMAGCGATGAGGAGVAGMDSSGC MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 40 nsites= 7 E= 4.0e-010 0.000000 0.857143 0.000000 0.142857 0.428571 0.000000 0.571429 0.000000 0.285714 0.142857 0.571429 0.000000 0.000000 0.714286 0.142857 0.142857 0.000000 0.000000 1.000000 0.000000 0.714286 0.000000 0.285714 0.000000 0.142857 0.857143 0.000000 0.000000 0.142857 0.142857 0.714286 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.142857 0.285714 0.571429 0.000000 0.000000 1.000000 0.000000 0.000000 0.428571 0.285714 0.285714 0.428571 0.285714 0.285714 0.000000 0.000000 0.000000 1.000000 0.000000 0.571429 0.142857 0.000000 0.285714 0.000000 0.142857 0.857143 0.000000 0.000000 0.571429 0.285714 0.142857 0.000000 0.285714 0.571429 0.142857 0.428571 0.571429 0.000000 0.000000 0.714286 0.142857 0.000000 0.142857 0.142857 0.000000 0.714286 0.142857 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.857143 0.000000 0.000000 0.142857 0.000000 0.142857 0.142857 0.714286 0.000000 0.000000 1.000000 0.000000 0.857143 0.000000 0.142857 0.000000 0.000000 0.142857 0.857143 0.000000 0.142857 0.000000 0.857143 0.000000 0.857143 0.142857 0.000000 0.000000 0.000000 0.000000 0.857143 0.142857 0.285714 0.285714 0.428571 0.000000 0.857143 0.000000 0.000000 0.142857 0.000000 0.000000 1.000000 0.000000 0.285714 0.571429 0.000000 0.142857 0.428571 0.000000 0.285714 0.285714 0.000000 0.285714 0.571429 0.142857 0.000000 0.571429 0.428571 0.000000 0.000000 0.285714 0.714286 0.000000 0.000000 1.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CRRCGACGAKGBVGWGSSMAGCGATGAGGAGVAGMDSSGC MEME-1 regular expression -------------------------------------------------------------------------------- C[GA][GA]CG[AG]CGA[TG]G[CGT][ACG]G[AT]G[CG][GC][CA]AGCGATGAGGAG[GAC]AG[CA][AGT][GC][CG][GC]C -------------------------------------------------------------------------------- Time 33.36 secs. ******************************************************************************** ******************************************************************************** MOTIF AKWATHWADDRKYWDATGTWMWYKWAWKHHTWWSRSGWYASGMTGC MEME-2 width = 46 sites = 3 llr = 140 E-value = 1.1e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif AKWATHWADDRKYWDATGTWMWYKWAWKHHTWWSRSGWYASGMTGC MEME-2 Description -------------------------------------------------------------------------------- Simplified A a:7a:37a337::73a:::777::3a3:33:33:7::7:a::3::: pos.-specific C :::::3::::::3:::::::3:7:::::33:::7:7::3:3:7::a probability G :3::::::3333::3::a:::::7:::3:::::333a:::7a::a: matrix T :73:a33:33:7733:a:a3:3337:7733a77::::37::::a:: bits 2.4 * ** * ** * * * * * 2.2 * ** * ** * * * * * 1.9 * ** * ** * * * * * 1.7 * ** * **** * * * * * *** Relative 1.4 * *** ** * ***** * *** *** ** * * *** Entropy 1.2 ***** ** **** ******* **** *** * **** * *** (67.5 bits) 1.0 ***** ** **** ************* *** * **** ***** 0.7 ***** ** **** ************* **************** 0.5 ********************************************** 0.2 ********************************************** 0.0 ---------------------------------------------- Multilevel ATAATAAAAAATTAAATGTAAACGTATTAATTTCACGATAGGCTGC consensus GT CT GGGGCTG TCTTTA AGCC AAGGG TC C A sequence T TT T TT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AKWATHWADDRKYWDATGTWMWYKWAWKHHTWWSRSGWYASGMTGC MEME-2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------------------------------------- cds-NP_214842.1 51 1.95e-22 CTCCCTTCTG ATAATCAAATGTTTGATGTAAACGAATGCTTATCACGATAGGATGC AGCT cds-NP_216501.1 31 7.69e-22 AGTCATATCG ATTATTAAGAAGTAAATGTAATCGTAATAATTACACGTCACGCTGC GAGGCGTCTA nmtR 49 3.34e-21 CCAACATATC AGAATATATGATCATATGTTCATTTATTTCTTTGGGGATAGGCTGC CTAACC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AKWATHWADDRKYWDATGTWMWYKWAWKHHTWWSRSGWYASGMTGC MEME-2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- cds-NP_214842.1 1.9e-22 50_[+2]_4 cds-NP_216501.1 7.7e-22 30_[+2]_24 nmtR 3.3e-21 48_[+2]_6 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AKWATHWADDRKYWDATGTWMWYKWAWKHHTWWSRSGWYASGMTGC MEME-2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF AKWATHWADDRKYWDATGTWMWYKWAWKHHTWWSRSGWYASGMTGC width=46 seqs=3 cds-NP_214842.1 ( 51) ATAATCAAATGTTTGATGTAAACGAATGCTTATCACGATAGGATGC 1 cds-NP_216501.1 ( 31) ATTATTAAGAAGTAAATGTAATCGTAATAATTACACGTCACGCTGC 1 nmtR ( 49) AGAATATATGATCATATGTTCATTTATTTCTTTGGGGATAGGCTGC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AKWATHWADDRKYWDATGTWMWYKWAWKHHTWWSRSGWYASGMTGC MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 46 n= 14850 bayes= 11.0501 E= 1.1e+001 232 -823 -823 -823 -823 -823 12 180 174 -823 -823 80 232 -823 -823 -823 -823 -823 -823 239 74 13 -823 80 174 -823 -823 80 232 -823 -823 -823 74 -823 12 80 74 -823 12 80 174 -823 12 -823 -823 -823 12 180 -823 13 -823 180 174 -823 -823 80 74 -823 12 80 232 -823 -823 -823 -823 -823 -823 239 -823 -823 171 -823 -823 -823 -823 239 174 -823 -823 80 174 13 -823 -823 174 -823 -823 80 -823 113 -823 80 -823 -823 112 80 74 -823 -823 180 232 -823 -823 -823 74 -823 -823 180 -823 -823 12 180 74 13 -823 80 74 13 -823 80 -823 -823 -823 239 74 -823 -823 180 74 -823 -823 180 -823 113 12 -823 174 -823 12 -823 -823 113 12 -823 -823 -823 171 -823 174 -823 -823 80 -823 13 -823 180 232 -823 -823 -823 -823 13 112 -823 -823 -823 171 -823 74 113 -823 -823 -823 -823 -823 239 -823 -823 171 -823 -823 171 -823 -823 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AKWATHWADDRKYWDATGTWMWYKWAWKHHTWWSRSGWYASGMTGC MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 46 nsites= 3 E= 1.1e+001 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.333333 0.666667 0.666667 0.000000 0.000000 0.333333 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.333333 0.333333 0.000000 0.333333 0.666667 0.000000 0.000000 0.333333 1.000000 0.000000 0.000000 0.000000 0.333333 0.000000 0.333333 0.333333 0.333333 0.000000 0.333333 0.333333 0.666667 0.000000 0.333333 0.000000 0.000000 0.000000 0.333333 0.666667 0.000000 0.333333 0.000000 0.666667 0.666667 0.000000 0.000000 0.333333 0.333333 0.000000 0.333333 0.333333 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 0.000000 0.000000 1.000000 0.666667 0.000000 0.000000 0.333333 0.666667 0.333333 0.000000 0.000000 0.666667 0.000000 0.000000 0.333333 0.000000 0.666667 0.000000 0.333333 0.000000 0.000000 0.666667 0.333333 0.333333 0.000000 0.000000 0.666667 1.000000 0.000000 0.000000 0.000000 0.333333 0.000000 0.000000 0.666667 0.000000 0.000000 0.333333 0.666667 0.333333 0.333333 0.000000 0.333333 0.333333 0.333333 0.000000 0.333333 0.000000 0.000000 0.000000 1.000000 0.333333 0.000000 0.000000 0.666667 0.333333 0.000000 0.000000 0.666667 0.000000 0.666667 0.333333 0.000000 0.666667 0.000000 0.333333 0.000000 0.000000 0.666667 0.333333 0.000000 0.000000 0.000000 1.000000 0.000000 0.666667 0.000000 0.000000 0.333333 0.000000 0.333333 0.000000 0.666667 1.000000 0.000000 0.000000 0.000000 0.000000 0.333333 0.666667 0.000000 0.000000 0.000000 1.000000 0.000000 0.333333 0.666667 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 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AKWATHWADDRKYWDATGTWMWYKWAWKHHTWWSRSGWYASGMTGC MEME-2 regular expression -------------------------------------------------------------------------------- A[TG][AT]AT[ACT][AT]A[AGT][AGT][AG][TG][TC][AT][AGT]ATGT[AT][AC][AT][CT][GT][TA]A[TA][TG][ACT][ACT]T[TA][TA][CG][AG][CG]G[AT][TC]A[GC]G[CA]TGC -------------------------------------------------------------------------------- Time 65.51 secs. ******************************************************************************** ******************************************************************************** MOTIF TCTTGCCTTTDACWTCBAYCA MEME-3 width = 21 sites = 5 llr = 106 E-value = 2.4e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif TCTTGCCTTTDACWTCBAYCA MEME-3 Description -------------------------------------------------------------------------------- Simplified A :2:::22:::2a:4:::8::8 pos.-specific C :62::86:::::a::84:4a: probability G 2:::a:::2:4:::2242::2 matrix T 828a::2a8a4::68:2:6:: bits 2.4 * * * * 2.2 * * * * 1.9 * * * * 1.7 ** * * ** * Relative 1.4 * *** *** **** * ** Entropy 1.2 * **** *** **** **** (30.5 bits) 1.0 * **** *** ***** **** 0.7 ********** ***** **** 0.5 **************** **** 0.2 ********************* 0.0 --------------------- Multilevel TCTTGCCTTTGACTTCCATCA consensus GAC AA G T AGGGGC G sequence T T A T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TCTTGCCTTTDACWTCBAYCA MEME-3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- smtB 8 3.14e-11 GGTCTCC TATTGCCTTTGACATGCATCA TCATGCATGT cds-NP_214556.1 70 4.33e-11 ACCTAGGCCG TCTTGACTGTTACATCCATCA GTCGGTACTG hrcA 49 5.86e-11 CACCGGCGGC TCTTGCATTTTACTTCGGCCA GTCCGTCGCA cds-NP_218347.1 72 3.54e-10 GTTACAACTG TCTTGCTTTTAACTGCTATCG AACGTCAG manB 63 5.33e-10 CGTCCAGGGC GTCTGCCTTTGACTTCGACCA TCTTCCCGCC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TCTTGCCTTTDACWTCBAYCA MEME-3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- smtB 3.1e-11 7_[+3]_72 cds-NP_214556.1 4.3e-11 69_[+3]_10 hrcA 5.9e-11 48_[+3]_31 cds-NP_218347.1 3.5e-10 71_[+3]_8 manB 5.3e-10 62_[+3]_17 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TCTTGCCTTTDACWTCBAYCA MEME-3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF TCTTGCCTTTDACWTCBAYCA width=21 seqs=5 smtB ( 8) TATTGCCTTTGACATGCATCA 1 cds-NP_214556.1 ( 70) TCTTGACTGTTACATCCATCA 1 hrcA ( 49) TCTTGCATTTTACTTCGGCCA 1 cds-NP_218347.1 ( 72) TCTTGCTTTTAACTGCTATCG 1 manB ( 63) GTCTGCCTTTGACTTCGACCA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TCTTGCCTTTDACWTCBAYCA MEME-3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 21600 bayes= 12.3281 E= 2.4e+001 -897 -897 -61 207 1 98 -897 7 -897 -60 -897 207 -897 -897 -897 239 -897 -897 171 -897 1 139 -897 -897 1 98 -897 7 -897 -897 -897 239 -897 -897 -61 207 -897 -897 -897 239 1 -897 39 107 233 -897 -897 -897 -897 171 -897 -897 100 -897 -897 165 -897 -897 -61 207 -897 139 -61 -897 -897 39 39 7 200 -897 -61 -897 -897 39 -897 165 -897 171 -897 -897 200 -897 -61 -897 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TCTTGCCTTTDACWTCBAYCA MEME-3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 5 E= 2.4e+001 0.000000 0.000000 0.200000 0.800000 0.200000 0.600000 0.000000 0.200000 0.000000 0.200000 0.000000 0.800000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.200000 0.800000 0.000000 0.000000 0.200000 0.600000 0.000000 0.200000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.200000 0.800000 0.000000 0.000000 0.000000 1.000000 0.200000 0.000000 0.400000 0.400000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.400000 0.000000 0.000000 0.600000 0.000000 0.000000 0.200000 0.800000 0.000000 0.800000 0.200000 0.000000 0.000000 0.400000 0.400000 0.200000 0.800000 0.000000 0.200000 0.000000 0.000000 0.400000 0.000000 0.600000 0.000000 1.000000 0.000000 0.000000 0.800000 0.000000 0.200000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TCTTGCCTTTDACWTCBAYCA MEME-3 regular expression -------------------------------------------------------------------------------- [TG][CAT][TC]TG[CA][CAT]T[TG]T[GTA]AC[TA][TG][CG][CGT][AG][TC]C[AG] -------------------------------------------------------------------------------- Time 97.21 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- dnaN 3.60e-01 100 cds-NP_214537.1 3.75e-01 100 cds-NP_214552.1 5.52e-01 100 cds-NP_214556.1 2.24e-07 69_[+3(4.33e-11)]_10 cds-NP_214557.1 2.95e-01 100 cds-NP_214561.1 5.64e-01 100 cds-NP_214566.3 5.95e-02 100 rpsF 8.56e-01 100 rpsR1 7.80e-01 100 rplI 1.42e-01 100 cds-NP_214581.1 9.47e-01 100 cds-NP_214592.1 4.11e-01 100 cds-NP_214595.1 2.03e-01 100 nrp 9.76e-01 100 rpmB1 2.43e-01 100 oxyS 4.41e-01 100 fusA2 1.87e-01 100 cds-NP_214649.1 3.63e-01 100 cds-NP_214658.1 5.01e-01 100 cds-NP_214672.1 4.50e-01 100 mce1R 6.08e-01 100 sigG 6.69e-01 100 cds-NP_214710.1 2.19e-01 100 cds-NP_214746.1 4.66e-01 100 cds-NP_214752.1 5.30e-01 100 cds-NP_214787.1 5.29e-02 100 cds-YP_177706.1 4.33e-02 100 cds-NP_214816.1 8.33e-02 100 cds-NP_214842.1 1.38e-18 50_[+2(1.95e-22)]_4 cds-NP_214844.1 1.86e-01 100 cds-NP_214891.1 4.68e-01 100 sigK 3.42e-01 100 cds-NP_214979.1 5.60e-01 100 cds-NP_214986.1 3.08e-01 100 cds-NP_214988.1 3.26e-02 100 cds-NP_214999.1 9.70e-01 100 cds-NP_215008.2 9.11e-01 100 mce2R 2.66e-01 100 cds-YP_177629.1 6.51e-01 100 rpmG2 7.69e-01 100 nusG 2.74e-01 100 rplK 8.43e-01 100 rplA 9.17e-01 100 cds-NP_215164.1 4.74e-01 100 rplJ 5.13e-01 100 rplL 8.75e-01 100 cds-NP_215167.1 5.90e-01 100 vapB6 5.57e-01 100 mazE2 7.57e-01 100 rpoB 5.61e-01 100 rpoC 4.33e-01 100 lpqP 6.51e-01 100 cds-NP_215188.1 1.54e-02 28_[+1(9.53e-05)]_32 rpsL 4.00e-01 100 rpsG 2.53e-01 100 fusA1 5.53e-02 100 tuf 2.42e-01 100 cds-NP_215205.1 4.54e-02 100 rpsJ 3.29e-02 23_[+1(5.05e-05)]_37 rplC 9.31e-02 100 rplD 1.86e-01 100 rplW 1.22e-08 16_[+1(1.25e-12)]_44 rplB 2.41e-17 10_[+1(3.96e-22)]_50 rpsS 9.71e-01 100 rplV 1.52e-01 100 rpsC 6.97e-01 100 rplP 4.48e-01 100 rpmC 9.17e-01 100 rpsQ 8.95e-01 100 rplN 8.72e-01 100 rplX 8.01e-01 100 rplE 8.37e-01 100 rpsN1 5.22e-01 100 rpsH 9.77e-11 3_[+1(8.97e-15)]_57 rplF 1.54e-01 100 rplR 2.57e-08 31_[+1(3.29e-12)]_29 rpsE 7.55e-01 100 rpmD 1.65e-01 100 rplO 9.41e-01 100 cds-NP_215244.1 2.80e-01 100 sigL 2.69e-01 100 rslA 9.57e-01 100 cds-NP_215251.1 1.02e-01 100 cds-NP_215281.1 9.80e-01 100 cds-NP_215307.1 1.66e-02 100 cds-NP_215317.1 3.88e-01 100 cds-NP_215337.1 8.96e-01 100 kmtR 8.79e-01 100 cds-NP_215395.1 7.20e-01 100 rimJ 8.37e-01 100 rplY 2.31e-01 100 cds-NP_215535.1 7.76e-01 100 mfd 1.64e-01 100 cds-NP_215560.1 4.14e-01 100 cds-NP_215565.1 4.54e-01 100 greA 1.35e-01 100 cds-NP_215628.1 3.51e-02 100 cds-NP_215645.1 5.03e-01 100 cds-NP_215668.1 4.47e-01 100 cds-NP_215683.1 8.52e-01 100 cds-NP_215692.1 4.77e-02 100 sigI 1.67e-01 100 cds-NP_215735.1 4.81e-01 100 sigE 9.10e-01 100 relE 6.03e-01 100 cds-NP_215771.1 5.34e-01 100 embR 5.17e-01 100 cds-NP_215803.1 5.16e-01 100 rho 9.12e-01 100 rpmE 7.26e-01 100 cds-NP_215817.1 3.59e-17 58_[+1(1.32e-21)]_2 atpB 6.39e-01 100 atpE 3.78e-02 100 atpF 3.05e-01 100 atpH 8.26e-01 100 atpA 9.95e-01 100 atpG 1.40e-09 6_[+1(4.16e-13)]_54 atpD 8.68e-01 100 atpC 5.54e-01 100 rpoZ 1.47e-01 100 cds-NP_215920.1 8.83e-02 100 cds-NP_215976.2 6.98e-01 100 cds-NP_215990.1 4.75e-01 100 cds-NP_216021.1 1.89e-01 100 cds-NP_216050.1 2.56e-01 100 dinX 5.04e-01 100 dnaE1 5.84e-01 100 cds-NP_216072.1 5.96e-01 100 vapB11 2.46e-01 100 cds-NP_216095.1 9.85e-01 100 polA 2.50e-01 100 rpsA 7.62e-01 100 infC 1.59e-01 100 rpmI 7.00e-01 100 rplT 5.92e-01 100 cds-NP_216201.1 8.50e-01 100 scpB 3.77e-14 58_[+1(2.14e-18)]_2 cds-NP_216235.1 6.11e-01 100 cds-NP_216241.1 2.67e-01 100 cds-NP_216289.1 5.63e-01 100 cds-NP_216344.1 7.13e-01 100 blaI 9.61e-01 100 cds-NP_216446.1 5.46e-01 100 cds-NP_216447.1 4.02e-01 100 parD1 8.50e-01 100 mce3R 7.85e-01 100 cds-NP_216501.1 2.29e-17 30_[+2(7.69e-22)]_24 mazE6 2.54e-01 100 cmtR 5.36e-02 100 vapB15 4.34e-01 100 cds-NP_216537.1 6.77e-01 100 cds-NP_216550.1 7.78e-01 100 rpsR2 7.90e-01 100 rpsN2 4.53e-01 100 rpmG1 1.08e-01 100 rpmB2 2.51e-01 100 sigC 9.44e-01 100 pafC 2.49e-01 100 pafB 7.94e-01 100 cds-NP_216648.1 3.40e-01 100 cds-NP_216707.1 6.59e-01 100 cds-NP_216766.2 3.31e-01 100 cds-NP_216798.1 8.55e-01 100 cds-NP_216840.1 1.94e-01 100 cds-NP_216843.1 7.90e-01 100 smtB 1.92e-07 7_[+3(3.14e-11)]_72 hrcA 3.24e-07 48_[+3(5.86e-11)]_31 cds-NP_216891.1 7.42e-01 100 mbtF 9.79e-01 100 mbtE 2.12e-01 100 mbtB 4.50e-01 100 rpsT 2.26e-01 100 cds-NP_216929.3 7.06e-01 100 rpmA 1.86e-01 100 rplU 6.89e-01 100 cds-NP_217022.1 1.61e-01 100 vapB17 4.43e-01 100 nusB 4.56e-02 100 efp 9.36e-01 100 vapB18 8.77e-01 100 fadD9 5.07e-02 100 cds-NP_217134.1 6.12e-02 100 cds-NP_217137.1 2.01e-02 36_[+2(1.51e-05)]_18 cds-NP_217156.1 1.51e-01 100 cds-NP_217158.1 8.73e-01 100 ppgK 6.09e-01 100 sigA 7.37e-01 100 cds-NP_217220.1 6.24e-01 100 sigB 6.42e-01 100 ideR 6.50e-01 100 nrdR 6.52e-01 100 lexA 4.11e-01 100 clgR 6.26e-01 100 vapB21 2.57e-01 100 cds-NP_217295.2 2.50e-01 100 rpsO 4.57e-01 100 sirR 8.60e-01 100 mazE9 3.31e-02 100 infB 5.93e-01 100 cds-NP_217356.3 4.54e-01 100 nusA 5.34e-01 100 relG 4.05e-01 100 cds-NP_217403.1 1.52e-01 100 tsf 4.81e-01 100 rpsB 7.78e-01 100 rplS 8.06e-01 100 rpsP 9.20e-01 100 cds-NP_217428.1 6.10e-01 100 tesA 3.43e-02 100 cds-YP_009030042.1 3.00e-01 100 cds-NP_217505.1 3.91e-01 100 cds-NP_217566.1 3.44e-01 100 cds-NP_217571.1 5.80e-02 50_[+2(9.79e-05)]_4 dinP 7.31e-01 100 cds-NP_217574.1 1.28e-01 100 cds-NP_217576.1 8.21e-01 100 pknK 4.79e-01 100 cds-NP_217611.1 8.72e-01 100 moaR1 3.46e-01 100 cds-NP_217676.1 1.63e-01 100 cds-NP_217683.1 9.63e-01 100 cds-NP_217689.1 6.35e-01 100 cds-NP_217699.1 7.78e-01 100 cds-NP_217724.1 6.61e-01 100 sigH 1.15e-01 100 cds-NP_217766.1 5.30e-01 100 manB 2.56e-06 62_[+3(5.33e-10)]_17 cds-NP_217784.1 3.86e-01 100 sigF 6.67e-01 100 lrpA 1.00e+00 100 cds-NP_217812.1 3.24e-01 100 lpqC 9.83e-01 100 sigJ 4.00e-01 100 cds-NP_217851.1 1.57e-01 100 dnaE2 8.44e-01 100 acrA1 1.84e-01 100 cds-NP_217911.1 8.95e-01 100 cds-NP_217922.1 1.40e-01 100 sigD 7.64e-02 100 rpsI 6.91e-01 100 rplM 2.45e-01 100 rplQ 4.89e-01 100 rpoA 3.04e-01 100 rpsD 5.16e-01 100 rpsK 7.90e-01 100 rpsM 4.21e-01 100 rpmJ 9.75e-01 100 infA 2.95e-01 100 cds-NP_218001.1 6.86e-01 100 cds-NP_218005.1 7.46e-01 100 cds-NP_218074.1 8.71e-01 100 kstR 4.02e-01 100 cds-NP_218092.1 7.74e-01 100 cds-NP_218100.1 5.80e-01 100 cds-NP_218117.1 4.86e-01 100 cds-NP_218161.1 4.42e-01 100 cds-NP_218192.1 5.66e-02 100 cds-NP_218195.1 2.79e-01 100 dnaQ 2.08e-01 100 dnaZX 1.76e-01 100 cds-NP_218239.2 5.01e-01 100 nmtR 3.67e-17 48_[+2(3.34e-21)]_6 cds-NP_218305.1 8.06e-01 100 cds-NP_218347.1 1.80e-06 71_[+3(3.54e-10)]_8 cds-NP_218350.1 7.17e-01 100 cds-NP_218357.1 8.85e-02 100 ethR 8.45e-01 100 pcnA 2.98e-01 100 sigM 3.73e-01 100 parB 8.40e-03 100 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (3) found. ******************************************************************************** CPU: kodomo ********************************************************************************