******************************************************************************** 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-NP_459019.1 1.0000 100 cds-NP_459035.1 1.0000 100 nhaR 1.0000 100 rpsT 1.0000 100 polB 1.0000 100 leuO 1.0000 100 fruR 1.0000 100 pdhR 1.0000 100 cds-NP_459169.1 1.0000 100 pcnB 1.0000 100 rpsB 1.0000 100 tsf 1.0000 100 dnaE 1.0000 100 rof 1.0000 100 yafC 1.0000 100 dnaQ 1.0000 100 sinR 1.0000 100 dinP 1.0000 100 cds-NP_459328.1 1.0000 100 cds-NP_459349.1 1.0000 100 prpR 1.0000 100 yajF 1.0000 100 cds-NP_459405.1 1.0000 100 ybaD 1.0000 100 nusB 1.0000 100 phnR 1.0000 100 ybaO 1.0000 100 rpmE2 1.0000 100 rpmJ2 1.0000 100 acrR 1.0000 100 dnaX 1.0000 100 cueR 1.0000 100 ybbS 1.0000 100 allR 1.0000 100 cds-NP_459563.1 1.0000 100 cds-NP_459572.1 1.0000 100 entF 1.0000 100 ybdO 1.0000 100 rnk 1.0000 100 ybeF 1.0000 100 holA 1.0000 100 cds-NP_459644.1 1.0000 100 nagC 1.0000 100 cds-NP_459677.1 1.0000 100 cds-NP_459743.3 1.0000 100 cds-NP_459744.1 1.0000 100 hutC 1.0000 100 ybiH 1.0000 100 cds-NP_459812.1 1.0000 100 cds-NP_459836.1 1.0000 100 deoR 1.0000 100 rimK 1.0000 100 cds-NP_459874.1 1.0000 100 cds-NP_459875.1 1.0000 100 cds-NP_459928.1 1.0000 100 infA 1.0000 100 lrp 1.0000 100 rpsA 1.0000 100 cds-NP_459976.1 1.0000 100 cds-NP_459987.1 1.0000 100 cds-NP_459988.1 1.0000 100 cds-NP_459991.1 1.0000 100 cds-NP_460004.1 1.0000 100 hpaR 1.0000 100 ycdC 1.0000 100 cds-NP_460099.1 1.0000 100 rimJ 1.0000 100 rpmF 1.0000 100 holB 1.0000 100 ycfQ 1.0000 100 mfd 1.0000 100 ycfX 1.0000 100 infC 1.0000 100 rpmI 1.0000 100 rplT 1.0000 100 orf242 1.0000 100 ydhB 1.0000 100 purR 1.0000 100 rnt 1.0000 100 ydhM 1.0000 100 slyA 1.0000 100 ynfL 1.0000 100 mlc 1.0000 100 speG 1.0000 100 ydfH 1.0000 100 marR 1.0000 100 yneJ 1.0000 100 cds-NP_460501.1 1.0000 100 cds-NP_460507.1 1.0000 100 cds-NP_460509.1 1.0000 100 cds-NP_460510.1 1.0000 100 cds-NP_460514.1 1.0000 100 cds-NP_460534.1 1.0000 100 yncC 1.0000 100 ydcR 1.0000 100 ydcN 1.0000 100 ydcK 1.0000 100 rimL 1.0000 100 cds-NP_460577.1 1.0000 100 ydcI 1.0000 100 cds-NP_460623.1 1.0000 100 cds-NP_460632.1 1.0000 100 cds-NP_460635.1 1.0000 100 tyrR 1.0000 100 pspC 1.0000 100 pspF 1.0000 100 yciT 1.0000 100 yciH 1.0000 100 cysB 1.0000 100 yciO 1.0000 100 ychF 1.0000 100 fadR 1.0000 100 yoaB 1.0000 100 kdgR 1.0000 100 exoX 1.0000 100 yebK 1.0000 100 fliA 1.0000 100 umuC 1.0000 100 umuD 1.0000 100 yeeY 1.0000 100 rfbF 1.0000 100 yegW 1.0000 100 cds-NP_461125.1 1.0000 100 galS 1.0000 100 yeiE 1.0000 100 yeiP 1.0000 100 rplY 1.0000 100 cds-NP_461173.3 1.0000 100 cds-NP_461217.3 1.0000 100 cds-NP_461223.1 1.0000 100 yfaX 1.0000 100 lrhA 1.0000 100 cds-NP_461287.1 1.0000 100 cds-NP_461303.1 1.0000 100 cds-NP_461316.1 1.0000 100 yfeD 1.0000 100 xapR 1.0000 100 yfeR 1.0000 100 ptsJ 1.0000 100 yfhP 1.0000 100 csiE 1.0000 100 yfhH 1.0000 100 cds-NP_461510.1 1.0000 100 cds-NP_461559.1 1.0000 100 cds-NP_461562.1 1.0000 100 cds-NP_461563.1 1.0000 100 rpoE 1.0000 100 yfiE 1.0000 100 rplS 1.0000 100 rpsP 1.0000 100 cds-NP_461665.1 1.0000 100 cds-NP_461671.1 1.0000 100 cds-NP_461675.1 1.0000 100 cds-NP_461676.1 1.0000 100 ygaE 1.0000 100 cds-NP_461723.1 1.0000 100 cds-NP_461729.1 1.0000 100 emrR 1.0000 100 srlR 1.0000 100 ygaA 1.0000 100 fhlA 1.0000 100 cds-NP_461833.1 1.0000 100 ygbI 1.0000 100 cds-NP_461841.1 1.0000 100 rpoS 1.0000 100 cds-NP_461876.3 1.0000 100 fucR 1.0000 100 gcvA 1.0000 100 galR 1.0000 100 cds-NP_461929.1 1.0000 100 lysR 1.0000 100 cds-NP_461937.1 1.0000 100 iciA 1.0000 100 cds-NP_462000.3 1.0000 100 gshB 1.0000 100 yqgE 1.0000 100 cds-NP_462014.1 1.0000 100 cds-NP_462036.1 1.0000 100 cca 1.0000 100 rpsU 1.0000 100 rpoD 1.0000 100 yqjI 1.0000 100 yhaJ 1.0000 100 tdcA 1.0000 100 agaR 1.0000 100 cds-NP_462175.1 1.0000 100 rpsO 1.0000 100 infB 1.0000 100 nusA 1.0000 100 greA 1.0000 100 rpmA 1.0000 100 rplU 1.0000 100 nlp 1.0000 100 yrbA 1.0000 100 rpoN 1.0000 100 nanK 1.0000 100 yhcK 1.0000 100 rpsI 1.0000 100 rplM 1.0000 100 cds-NP_462267.1 1.0000 100 cds-NP_462268.1 1.0000 100 yhcS 1.0000 100 prmA 1.0000 100 fis 1.0000 100 envR 1.0000 100 zntR 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 rplO 1.0000 100 rpmD 1.0000 100 rpsE 1.0000 100 rplR 1.0000 100 rplF 1.0000 100 rpsH 1.0000 100 rpsN 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 tufA 1.0000 100 fusA 1.0000 100 rpsG 1.0000 100 rpsL 1.0000 100 greB 1.0000 100 yhgF 1.0000 100 malT 1.0000 100 rtcR 1.0000 100 glpR 1.0000 100 cds-NP_462434.1 1.0000 100 gntR 1.0000 100 rpoH 1.0000 100 nikR 1.0000 100 cds-NP_462503.1 1.0000 100 yhjC 1.0000 100 cds-NP_462535.1 1.0000 100 yiaG 1.0000 100 yiaJ 1.0000 100 cds-NP_462581.1 1.0000 100 selB 1.0000 100 mtlR 1.0000 100 lldR 1.0000 100 cds-NP_462596.1 1.0000 100 rpmG 1.0000 100 rpmB 1.0000 100 ttk 1.0000 100 cds-NP_462636.1 1.0000 100 rpoZ 1.0000 100 cds-NP_462672.1 1.0000 100 cds-NP_462677.1 1.0000 100 cds-NP_462684.1 1.0000 100 cds-NP_462693.1 1.0000 100 dsdC 1.0000 100 dgoR 1.0000 100 cds-NP_462734.1 1.0000 100 dnaN 1.0000 100 yidZ 1.0000 100 atpC 1.0000 100 atpD 1.0000 100 atpG 1.0000 100 atpA 1.0000 100 atpH 1.0000 100 atpF 1.0000 100 atpE 1.0000 100 atpB 1.0000 100 atpI 1.0000 100 asnC 1.0000 100 rbsR 1.0000 100 yieP 1.0000 100 yifA 1.0000 100 ilvY 1.0000 100 rho 1.0000 100 metR 1.0000 100 rfaH 1.0000 100 polA 1.0000 100 yihW 1.0000 100 cds-NP_462910.3 1.0000 100 cds-NP_462913.3 1.0000 100 cds-NP_462923.1 1.0000 100 cds-NP_462949.1 1.0000 100 ydeW 1.0000 100 cytR 1.0000 100 rpmE 1.0000 100 metJ 1.0000 100 oxyR 1.0000 100 tufB 1.0000 100 nusG 1.0000 100 rplK 1.0000 100 rplA 1.0000 100 rplJ 1.0000 100 rplL 1.0000 100 rpoB 1.0000 100 rpoC 1.0000 100 iclR 1.0000 100 lexA 1.0000 100 soxR 1.0000 100 cds-NP_463135.1 1.0000 100 cds-NP_463185.1 1.0000 100 efp 1.0000 100 yjeB 1.0000 100 yjfQ 1.0000 100 rpsF 1.0000 100 rpsR 1.0000 100 rplI 1.0000 100 ytfH 1.0000 100 ytfJ 1.0000 100 cds-NP_463278.1 1.0000 100 cds-NP_463309.1 1.0000 100 cds-NP_463311.1 1.0000 100 treR 1.0000 100 yjgF 1.0000 100 holC 1.0000 100 idnR 1.0000 100 uxuR 1.0000 100 yjiE 1.0000 100 cds-NP_463393.1 1.0000 100 holD 1.0000 100 cds-NP_490539.1 1.0000 100 samB_2 1.0000 100 samA 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 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= 8 maxw= 50 nsites: minsites= 2 maxsites= 333 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= 33300 N= 333 sample: seed= 0 hsfrac= 0 searchsize= 33300 norand= no csites= 1000 Letter frequencies in dataset: A 0.275 C 0.226 G 0.219 T 0.28 Background letter frequencies (from file dataset with add-one prior applied): A 0.275 C 0.226 G 0.219 T 0.28 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF MDSNGCCSCCGCNGGCGSADA MEME-1 width = 21 sites = 11 llr = 169 E-value = 1.1e+000 ******************************************************************************** -------------------------------------------------------------------------------- Motif MDSNGCCSCCGCNGGCGSADA MEME-1 Description -------------------------------------------------------------------------------- Simplified A 44:3:::21:::2:2::2538 pos.-specific C 6153:6a486283:1a13211 probability G :25293:513822a7:9514: matrix T :4:311:::1::4:::::231 bits 2.2 * * * 2.0 * * * 1.8 * * * ** 1.5 * * ** * ** Relative 1.3 * * * ** * ** Entropy 1.1 * * * * * ** **** * (22.2 bits) 0.9 * * *** **** **** * 0.7 * * ******** ***** * 0.4 * * ******** ***** * 0.2 *** ******** ******** 0.0 --------------------- Multilevel CACAGCCGCCGCTGGCGGAGA consensus ATGC G C G C C A sequence T T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif MDSNGCCSCCGCNGGCGSADA MEME-1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- holA 45 3.59e-12 GCGGCTGTTA CTCTGCCGCCGCGGGCGGAGA TGCGGTCGTG cds-NP_459644.1 12 2.65e-09 GTAAACTGAA CCCAGCCGCCGCAGGCGGTTA GCGTTTCGGC atpD 51 6.80e-09 GTGGCTCTAG CAGAGCCCCCGGCGGCGCCAA ATTGGTCCAA mtlR 16 1.74e-08 GAAAAAGGCC CGCAGGCCGCGCTGGCGCAAA TTTCCGGGCT nanK 24 2.12e-08 GCGTACCCGC CACTGCCACCCCAGGCGGTAA TGGGCAGACC rpsF 47 9.95e-08 CCTTGCCTCC ATGGGCCGCGGCTGACCCAGA CAGGAGGCTG ycfX 17 1.25e-07 GCGAGCTGGT ATCCGGCGCGGCGGGCGAGCA ACATTGACCC ycdC 13 1.25e-07 AAAAAGTGTC ATGCGCCACCGCCGCCGGATT TCCGGCGGTT cds-NP_462949.1 65 1.79e-07 GGGACGGTAA AACGTCCCCTGCTGGCGAAGA CGTGAGGTGC hutC 1 1.92e-07 . CAGCGGCGCGCGTGGCGGCGC GGCTTGGCTG cds-NP_461929.1 44 2.35e-07 CGCCGACATT CGGTGTCCACGCCGACGGATA CCGGGCACCT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif MDSNGCCSCCGCNGGCGSADA MEME-1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- holA 3.6e-12 44_[+1]_35 cds-NP_459644.1 2.6e-09 11_[+1]_68 atpD 6.8e-09 50_[+1]_29 mtlR 1.7e-08 15_[+1]_64 nanK 2.1e-08 23_[+1]_56 rpsF 1e-07 46_[+1]_33 ycfX 1.2e-07 16_[+1]_63 ycdC 1.2e-07 12_[+1]_67 cds-NP_462949.1 1.8e-07 64_[+1]_15 hutC 1.9e-07 [+1]_79 cds-NP_461929.1 2.4e-07 43_[+1]_36 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif MDSNGCCSCCGCNGGCGSADA MEME-1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF MDSNGCCSCCGCNGGCGSADA width=21 seqs=11 holA ( 45) CTCTGCCGCCGCGGGCGGAGA 1 cds-NP_459644.1 ( 12) CCCAGCCGCCGCAGGCGGTTA 1 atpD ( 51) CAGAGCCCCCGGCGGCGCCAA 1 mtlR ( 16) CGCAGGCCGCGCTGGCGCAAA 1 nanK ( 24) CACTGCCACCCCAGGCGGTAA 1 rpsF ( 47) ATGGGCCGCGGCTGACCCAGA 1 ycfX ( 17) ATCCGGCGCGGCGGGCGAGCA 1 ycdC ( 13) ATGCGCCACCGCCGCCGGATT 1 cds-NP_462949.1 ( 65) AACGTCCCCTGCTGGCGAAGA 1 hutC ( 1) CAGCGGCGCGCGTGGCGGCGC 1 cds-NP_461929.1 ( 44) CGGTGTCCACGCCGACGGATA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif MDSNGCCSCCGCNGGCGSADA MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 26640 bayes= 12.2681 E= 1.1e+000 40 150 -1010 -1010 40 -131 -27 37 -1010 127 106 -1010 -1 27 -27 -4 -1010 -1010 205 -162 -1010 150 32 -162 -1010 215 -1010 -1010 -60 69 106 -1010 -160 186 -126 -1010 -1010 150 32 -162 -1010 -31 190 -1010 -1010 186 -27 -1010 -60 27 -27 37 -1010 -1010 219 -1010 -60 -131 173 -1010 -1010 215 -1010 -1010 -1010 -131 205 -1010 -60 27 132 -1010 99 -31 -126 -62 -1 -131 73 -4 157 -131 -1010 -162 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif MDSNGCCSCCGCNGGCGSADA MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 11 E= 1.1e+000 0.363636 0.636364 0.000000 0.000000 0.363636 0.090909 0.181818 0.363636 0.000000 0.545455 0.454545 0.000000 0.272727 0.272727 0.181818 0.272727 0.000000 0.000000 0.909091 0.090909 0.000000 0.636364 0.272727 0.090909 0.000000 1.000000 0.000000 0.000000 0.181818 0.363636 0.454545 0.000000 0.090909 0.818182 0.090909 0.000000 0.000000 0.636364 0.272727 0.090909 0.000000 0.181818 0.818182 0.000000 0.000000 0.818182 0.181818 0.000000 0.181818 0.272727 0.181818 0.363636 0.000000 0.000000 1.000000 0.000000 0.181818 0.090909 0.727273 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.090909 0.909091 0.000000 0.181818 0.272727 0.545455 0.000000 0.545455 0.181818 0.090909 0.181818 0.272727 0.090909 0.363636 0.272727 0.818182 0.090909 0.000000 0.090909 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif MDSNGCCSCCGCNGGCGSADA MEME-1 regular expression -------------------------------------------------------------------------------- [CA][AT][CG][ACT]G[CG]C[GC]C[CG]GC[TC]GGCG[GC]A[GAT]A -------------------------------------------------------------------------------- Time 43.21 secs. ******************************************************************************** ******************************************************************************** MOTIF AAARBCGCVSWHVCBNCCVTTNCCGVSMKTGAAGTGAT MEME-2 width = 38 sites = 5 llr = 153 E-value = 3.4e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif AAARBCGCVSWHVCBNCCVTTNCCGVSMKTGAAGTGAT MEME-2 Description -------------------------------------------------------------------------------- Simplified A a8a4::::4:644::2::4::4:::4:4:2:a822:8: pos.-specific C :2::48:a24:44842a82::2a82446:22:::2:2: probability G :::64:a:46::2:24:24222:2626:4:8:28:a:2 matrix T ::::22::::42:242:::882::2:::66::::6::8 bits 2.2 ** * * * 2.0 ** * * * 1.8 * * ** * * * * 1.5 * * ** ** ** ** * Relative 1.3 * * *** * ** ** ** * * Entropy 1.1 **** *** * * ** ** ** *** **** *** (44.1 bits) 0.9 **** *** ** * ** ** ** *** **** *** 0.7 ******** ** * ** ** *** *** **** *** 0.4 *************** ***** **************** 0.2 ********************* **************** 0.0 -------------------------------------- Multilevel AAAGCCGCAGAAACCGCCATTACCGAGCTTGAAGTGAT consensus C AGT GCTCCTTA GGGGC GCCCAGAC GAA CG sequence T C TG GC C G TG C C T T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAARBCGCVSWHVCBNCCVTTNCCGVSMKTGAAGTGAT MEME-2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------------------------------------- nusB 15 1.09e-15 AGCCGGTAAT AAAGGCGCAGAAGCTGCGCTGACCGCGCTTGAAATGAT TAATGTATTG malT 59 3.68e-15 AAGCGCAAAA AAAATCGCAGTTCCCCCCATTTCCCACAGTGAAGTGAT TGCT rbsR 32 6.93e-15 CGTAACGCGT AAAGGCGCGCAACCTTCCGTTCCGTGGCGCGAAGAGAT AGAAGCGTTT gshB 25 2.46e-14 GCGTACTGAG ACAACCGCGCTCACCGCCATTACCGCGCTACAGGTGCG TTTTGGCGAC rplA 5 3.99e-14 GACC AAAGCTGCCGACATGACCGGTGCCGACATTGAAGCGAT GACTCGCTCC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAARBCGCVSWHVCBNCCVTTNCCGVSMKTGAAGTGAT MEME-2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- nusB 1.1e-15 14_[+2]_48 malT 3.7e-15 58_[+2]_4 rbsR 6.9e-15 31_[+2]_31 gshB 2.5e-14 24_[+2]_38 rplA 4e-14 4_[+2]_58 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAARBCGCVSWHVCBNCCVTTNCCGVSMKTGAAGTGAT MEME-2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF AAARBCGCVSWHVCBNCCVTTNCCGVSMKTGAAGTGAT width=38 seqs=5 nusB ( 15) AAAGGCGCAGAAGCTGCGCTGACCGCGCTTGAAATGAT 1 malT ( 59) AAAATCGCAGTTCCCCCCATTTCCCACAGTGAAGTGAT 1 rbsR ( 32) AAAGGCGCGCAACCTTCCGTTCCGTGGCGCGAAGAGAT 1 gshB ( 25) ACAACCGCGCTCACCGCCATTACCGCGCTACAGGTGCG 1 rplA ( 5) AAAGCTGCCGACATGACCGGTGCCGACATTGAAGCGAT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAARBCGCVSWHVCBNCCVTTNCCGVSMKTGAAGTGAT MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 38 n= 20979 bayes= 12.286 E= 3.4e+001 186 -897 -897 -897 154 -17 -897 -897 186 -897 -897 -897 54 -897 145 -897 -897 83 87 -49 -897 182 -897 -49 -897 -897 219 -897 -897 215 -897 -897 54 -17 87 -897 -897 83 145 -897 112 -897 -897 51 54 83 -897 -49 54 83 -13 -897 -897 182 -897 -49 -897 83 -13 51 -46 -17 87 -49 -897 215 -897 -897 -897 182 -13 -897 54 -17 87 -897 -897 -897 -13 151 -897 -897 -13 151 54 -17 -13 -49 -897 215 -897 -897 -897 182 -13 -897 -897 -17 145 -49 54 83 -13 -897 -897 83 145 -897 54 141 -897 -897 -897 -897 87 110 -46 -17 -897 110 -897 -17 187 -897 186 -897 -897 -897 154 -897 -13 -897 -46 -897 187 -897 -46 -17 -897 110 -897 -897 219 -897 154 -17 -897 -897 -897 -897 -13 151 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAARBCGCVSWHVCBNCCVTTNCCGVSMKTGAAGTGAT MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 38 nsites= 5 E= 3.4e+001 1.000000 0.000000 0.000000 0.000000 0.800000 0.200000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.400000 0.000000 0.600000 0.000000 0.000000 0.400000 0.400000 0.200000 0.000000 0.800000 0.000000 0.200000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.400000 0.200000 0.400000 0.000000 0.000000 0.400000 0.600000 0.000000 0.600000 0.000000 0.000000 0.400000 0.400000 0.400000 0.000000 0.200000 0.400000 0.400000 0.200000 0.000000 0.000000 0.800000 0.000000 0.200000 0.000000 0.400000 0.200000 0.400000 0.200000 0.200000 0.400000 0.200000 0.000000 1.000000 0.000000 0.000000 0.000000 0.800000 0.200000 0.000000 0.400000 0.200000 0.400000 0.000000 0.000000 0.000000 0.200000 0.800000 0.000000 0.000000 0.200000 0.800000 0.400000 0.200000 0.200000 0.200000 0.000000 1.000000 0.000000 0.000000 0.000000 0.800000 0.200000 0.000000 0.000000 0.200000 0.600000 0.200000 0.400000 0.400000 0.200000 0.000000 0.000000 0.400000 0.600000 0.000000 0.400000 0.600000 0.000000 0.000000 0.000000 0.000000 0.400000 0.600000 0.200000 0.200000 0.000000 0.600000 0.000000 0.200000 0.800000 0.000000 1.000000 0.000000 0.000000 0.000000 0.800000 0.000000 0.200000 0.000000 0.200000 0.000000 0.800000 0.000000 0.200000 0.200000 0.000000 0.600000 0.000000 0.000000 1.000000 0.000000 0.800000 0.200000 0.000000 0.000000 0.000000 0.000000 0.200000 0.800000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAARBCGCVSWHVCBNCCVTTNCCGVSMKTGAAGTGAT MEME-2 regular expression -------------------------------------------------------------------------------- A[AC]A[GA][CGT][CT]GC[AGC][GC][AT][ACT][ACG][CT][CTG][GACT]C[CG][AGC][TG][TG][ACGT]C[CG][GCT][ACG][GC][CA][TG][TAC][GC]A[AG][GA][TAC]G[AC][TG] -------------------------------------------------------------------------------- Time 83.27 secs. ******************************************************************************** ******************************************************************************** MOTIF AMAAAAAYGRMGAYTDSYAMHATWCMSAVWRCYRCSNCGNSCNANTCK MEME-3 width = 48 sites = 6 llr = 190 E-value = 1.7e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif AMAAAAAYGRMGAYTDSYAMHATWCMSAVWRCYRCSNCGNSCNANTCK MEME-3 Description -------------------------------------------------------------------------------- Simplified A 85a887a::77:82232:8337:7:3:7375::5::3:2322373:2: pos.-specific C 23:::::52:3::5::35:73:2:85523:285:832823382:228: probability G :2:222::83:a2::3522::22:::5:3:3223272:725:323::7 matrix T :::::2:5:::::383:3::327322:2:3::32::32:2::2228:3 bits 2.2 * 2.0 * 1.8 * * * 1.5 * * * * * * * * * * Relative 1.3 * *** * * ** * * * ** * * ** Entropy 1.1 * *** ******* * ** * * * ** * * *** (45.6 bits) 0.9 * *** ******* * ** ** * * * ** ** * *** 0.7 ************* * **** **** ** **** ** ** ** * *** 0.4 ************************************ ** ** * *** 0.2 ************************************ ** ** * *** 0.0 ------------------------------------------------ Multilevel AAAAAAACGAAGACTAGCACAATACCCAAAACCACGACGAGCAAATCG consensus C T GC T GCT AC T AG CTG TG CT CC G G T sequence T T G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AMAAAAAYGRMGAYTDSYAMHATWCMSAVWRCYRCSNCGNSCNANTCK MEME-3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------------------------------------------ greA 1 7.29e-19 . AAAAAAACGAAGACTGGGACCATACCGTATACGGCCCCGACCGAATCG TCGGCCCCAT atpB 10 8.83e-18 ATTTCCGCC ACAAAAACGGCGACTAGCAATGCACCCAAAACCACGACCACCAAGTCT ATGACCGCGG rplF 4 2.63e-16 TCA ACAAAGATGGAGATTTCCACAATACTGACTAGCACGTCGCGCGGTCCG ACCAGAACCA rimJ 3 2.16e-14 TT CAAAAAATGACGATTTGCGCTTTTCACAGAGCCTGGTTGCGCAAGTAT AGTAATGTTA atpE 2 1.34e-13 T AAAAGTACCAAGACTGCTAACAGATAGACAGCTACCGCAGGCTTCTCG TAATTAAATG yhaJ 8 1.57e-13 TAATTGG AGAGAAATGAAGGAAAATACAATTCCCCGACCTGCGACGTAACAATCG GTCTATAAGA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AMAAAAAYGRMGAYTDSYAMHATWCMSAVWRCYRCSNCGNSCNANTCK MEME-3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- greA 7.3e-19 [+3]_52 atpB 8.8e-18 9_[+3]_43 rplF 2.6e-16 3_[+3]_49 rimJ 2.2e-14 2_[+3]_50 atpE 1.3e-13 1_[+3]_51 yhaJ 1.6e-13 7_[+3]_45 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AMAAAAAYGRMGAYTDSYAMHATWCMSAVWRCYRCSNCGNSCNANTCK MEME-3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF AMAAAAAYGRMGAYTDSYAMHATWCMSAVWRCYRCSNCGNSCNANTCK width=48 seqs=6 greA ( 1) AAAAAAACGAAGACTGGGACCATACCGTATACGGCCCCGACCGAATCG 1 atpB ( 10) ACAAAAACGGCGACTAGCAATGCACCCAAAACCACGACCACCAAGTCT 1 rplF ( 4) ACAAAGATGGAGATTTCCACAATACTGACTAGCACGTCGCGCGGTCCG 1 rimJ ( 3) CAAAAAATGACGATTTGCGCTTTTCACAGAGCCTGGTTGCGCAAGTAT 1 atpE ( 2) AAAAGTACCAAGACTGCTAACAGATAGACAGCTACCGCAGGCTTCTCG 1 yhaJ ( 8) AGAGAAATGAAGGAAAATACAATTCCCCGACCTGCGACGTAACAATCG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AMAAAAAYGRMGAYTDSYAMHATWCMSAVWRCYRCSNCGNSCNANTCK MEME-3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 48 n= 17649 bayes= 11.9694 E= 1.7e+001 160 -44 -923 -923 86 56 -39 -923 186 -923 -923 -923 160 -923 -39 -923 160 -923 -39 -923 127 -923 -39 -75 186 -923 -923 -923 -923 115 -923 83 -923 -44 193 -923 127 -923 61 -923 127 56 -923 -923 -923 -923 219 -923 160 -923 -39 -923 -72 115 -923 25 -72 -923 -923 157 28 -923 61 25 -72 56 119 -923 -923 115 -39 25 160 -923 -39 -923 28 156 -923 -923 28 56 -923 25 127 -923 -39 -75 -923 -44 -39 125 127 -923 -923 25 -923 188 -923 -75 28 115 -923 -75 -923 115 119 -923 127 -44 -923 -75 28 56 61 -923 127 -923 -923 25 86 -44 61 -923 -923 188 -39 -923 -923 115 -39 25 86 -923 61 -75 -923 188 -39 -923 -923 56 161 -923 28 -44 -39 25 -923 188 -923 -75 -72 -44 161 -923 28 56 -39 -75 -72 56 119 -923 -72 188 -923 -923 28 -44 61 -75 127 -923 -39 -75 28 -44 61 -75 -923 -44 -923 157 -72 188 -923 -923 -923 -923 161 25 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AMAAAAAYGRMGAYTDSYAMHATWCMSAVWRCYRCSNCGNSCNANTCK MEME-3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 48 nsites= 6 E= 1.7e+001 0.833333 0.166667 0.000000 0.000000 0.500000 0.333333 0.166667 0.000000 1.000000 0.000000 0.000000 0.000000 0.833333 0.000000 0.166667 0.000000 0.833333 0.000000 0.166667 0.000000 0.666667 0.000000 0.166667 0.166667 1.000000 0.000000 0.000000 0.000000 0.000000 0.500000 0.000000 0.500000 0.000000 0.166667 0.833333 0.000000 0.666667 0.000000 0.333333 0.000000 0.666667 0.333333 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.833333 0.000000 0.166667 0.000000 0.166667 0.500000 0.000000 0.333333 0.166667 0.000000 0.000000 0.833333 0.333333 0.000000 0.333333 0.333333 0.166667 0.333333 0.500000 0.000000 0.000000 0.500000 0.166667 0.333333 0.833333 0.000000 0.166667 0.000000 0.333333 0.666667 0.000000 0.000000 0.333333 0.333333 0.000000 0.333333 0.666667 0.000000 0.166667 0.166667 0.000000 0.166667 0.166667 0.666667 0.666667 0.000000 0.000000 0.333333 0.000000 0.833333 0.000000 0.166667 0.333333 0.500000 0.000000 0.166667 0.000000 0.500000 0.500000 0.000000 0.666667 0.166667 0.000000 0.166667 0.333333 0.333333 0.333333 0.000000 0.666667 0.000000 0.000000 0.333333 0.500000 0.166667 0.333333 0.000000 0.000000 0.833333 0.166667 0.000000 0.000000 0.500000 0.166667 0.333333 0.500000 0.000000 0.333333 0.166667 0.000000 0.833333 0.166667 0.000000 0.000000 0.333333 0.666667 0.000000 0.333333 0.166667 0.166667 0.333333 0.000000 0.833333 0.000000 0.166667 0.166667 0.166667 0.666667 0.000000 0.333333 0.333333 0.166667 0.166667 0.166667 0.333333 0.500000 0.000000 0.166667 0.833333 0.000000 0.000000 0.333333 0.166667 0.333333 0.166667 0.666667 0.000000 0.166667 0.166667 0.333333 0.166667 0.333333 0.166667 0.000000 0.166667 0.000000 0.833333 0.166667 0.833333 0.000000 0.000000 0.000000 0.000000 0.666667 0.333333 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AMAAAAAYGRMGAYTDSYAMHATWCMSAVWRCYRCSNCGNSCNANTCK MEME-3 regular expression -------------------------------------------------------------------------------- A[AC]AAAAA[CT]G[AG][AC]GA[CT]T[AGT][GC][CT]A[CA][ACT]AT[AT]C[CA][CG]A[ACG][AT][AG]C[CT][AG]C[GC][AT]CG[AC][GC]C[AG]A[AG]TC[GT] -------------------------------------------------------------------------------- Time 122.52 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- cds-NP_459019.1 1.00e+00 100 cds-NP_459035.1 9.54e-01 100 nhaR 3.00e-01 100 rpsT 9.74e-01 100 polB 8.47e-01 100 leuO 9.26e-01 100 fruR 3.14e-01 100 pdhR 7.36e-01 100 cds-NP_459169.1 8.13e-02 100 pcnB 2.20e-01 100 rpsB 7.24e-01 100 tsf 7.11e-01 100 dnaE 1.83e-01 100 rof 2.68e-01 100 yafC 9.97e-01 100 dnaQ 4.52e-01 100 sinR 8.07e-01 100 dinP 9.28e-01 100 cds-NP_459328.1 8.82e-01 100 cds-NP_459349.1 1.62e-01 100 prpR 9.61e-01 100 yajF 3.66e-01 100 cds-NP_459405.1 4.21e-01 100 ybaD 3.40e-01 100 nusB 4.00e-13 14_[+2(1.09e-15)]_48 phnR 3.61e-01 100 ybaO 6.55e-01 100 rpmE2 6.50e-01 100 rpmJ2 3.71e-01 100 acrR 1.00e+00 100 dnaX 7.99e-01 100 cueR 9.84e-01 100 ybbS 1.00e+00 100 allR 9.33e-01 100 cds-NP_459563.1 6.77e-01 100 cds-NP_459572.1 1.34e-01 100 entF 3.00e-01 100 ybdO 9.63e-01 100 rnk 5.90e-01 100 ybeF 9.89e-01 100 holA 2.48e-11 23_[+1(4.20e-05)]_[+1(3.59e-12)]_35 cds-NP_459644.1 5.69e-08 11_[+1(2.65e-09)]_68 nagC 6.82e-01 100 cds-NP_459677.1 1.75e-03 21_[+3(5.71e-05)]_31 cds-NP_459743.3 1.00e+00 100 cds-NP_459744.1 2.68e-01 100 hutC 1.17e-04 [+1(1.92e-07)]_79 ybiH 1.00e+00 100 cds-NP_459812.1 6.61e-01 100 cds-NP_459836.1 8.95e-01 100 deoR 5.22e-01 100 rimK 8.78e-02 100 cds-NP_459874.1 9.10e-01 100 cds-NP_459875.1 9.98e-01 100 cds-NP_459928.1 4.37e-01 100 infA 9.44e-01 100 lrp 9.10e-01 100 rpsA 1.40e-01 100 cds-NP_459976.1 6.46e-02 100 cds-NP_459987.1 8.93e-01 100 cds-NP_459988.1 2.04e-01 100 cds-NP_459991.1 3.46e-01 100 cds-NP_460004.1 4.45e-02 100 hpaR 6.50e-01 100 ycdC 3.09e-05 12_[+1(1.25e-07)]_67 cds-NP_460099.1 1.06e-01 100 rimJ 3.73e-11 2_[+3(2.16e-14)]_50 rpmF 5.35e-01 100 holB 1.54e-02 30_[+1(4.49e-05)]_49 ycfQ 7.17e-01 100 mfd 4.82e-01 100 ycfX 4.66e-05 16_[+1(1.25e-07)]_63 infC 1.89e-01 100 rpmI 9.69e-01 100 rplT 1.49e-01 100 orf242 7.42e-01 100 ydhB 9.29e-01 100 purR 4.78e-01 100 rnt 1.10e-01 100 ydhM 6.44e-01 100 slyA 6.77e-01 100 ynfL 6.11e-01 100 mlc 5.85e-01 100 speG 3.33e-01 100 ydfH 4.35e-01 100 marR 9.58e-01 100 yneJ 5.80e-01 100 cds-NP_460501.1 1.30e-01 100 cds-NP_460507.1 2.17e-01 100 cds-NP_460509.1 3.38e-01 100 cds-NP_460510.1 7.70e-01 100 cds-NP_460514.1 7.67e-01 100 cds-NP_460534.1 5.29e-01 100 yncC 1.53e-01 100 ydcR 3.65e-01 100 ydcN 5.39e-01 100 ydcK 9.68e-01 100 rimL 9.83e-01 100 cds-NP_460577.1 8.82e-01 100 ydcI 6.23e-01 100 cds-NP_460623.1 1.98e-01 100 cds-NP_460632.1 9.82e-01 100 cds-NP_460635.1 4.23e-01 100 tyrR 8.88e-01 100 pspC 7.78e-01 100 pspF 8.72e-01 100 yciT 1.63e-01 100 yciH 2.07e-01 100 cysB 5.21e-01 100 yciO 1.02e-01 100 ychF 1.87e-01 100 fadR 3.08e-02 100 yoaB 1.20e-03 29_[+1(2.78e-05)]_50 kdgR 8.77e-01 100 exoX 8.05e-01 100 yebK 5.25e-01 100 fliA 6.53e-01 100 umuC 6.71e-01 100 umuD 8.41e-01 100 yeeY 3.64e-01 100 rfbF 6.93e-01 100 yegW 1.69e-01 100 cds-NP_461125.1 9.52e-01 100 galS 3.72e-01 100 yeiE 8.06e-01 100 yeiP 9.29e-01 100 rplY 5.58e-01 100 cds-NP_461173.3 2.58e-01 100 cds-NP_461217.3 9.87e-01 100 cds-NP_461223.1 9.90e-01 100 yfaX 2.11e-01 100 lrhA 6.91e-01 100 cds-NP_461287.1 3.82e-03 6_[+2(5.96e-05)]_56 cds-NP_461303.1 4.76e-01 100 cds-NP_461316.1 7.22e-01 100 yfeD 3.72e-01 100 xapR 5.86e-01 100 yfeR 3.02e-01 100 ptsJ 4.34e-01 100 yfhP 6.46e-01 100 csiE 1.24e-01 100 yfhH 8.23e-01 100 cds-NP_461510.1 9.80e-01 100 cds-NP_461559.1 6.41e-01 100 cds-NP_461562.1 4.72e-01 100 cds-NP_461563.1 9.68e-01 100 rpoE 1.95e-01 100 yfiE 8.80e-01 100 rplS 6.97e-01 100 rpsP 2.62e-03 57_[+1(3.54e-05)]_22 cds-NP_461665.1 9.98e-01 100 cds-NP_461671.1 4.55e-02 100 cds-NP_461675.1 5.00e-01 100 cds-NP_461676.1 9.97e-01 100 ygaE 7.68e-02 100 cds-NP_461723.1 9.98e-01 100 cds-NP_461729.1 8.28e-01 100 emrR 1.00e+00 100 srlR 4.82e-01 100 ygaA 9.99e-01 100 fhlA 3.94e-01 100 cds-NP_461833.1 4.83e-02 100 ygbI 5.94e-01 100 cds-NP_461841.1 6.24e-01 100 rpoS 4.19e-01 100 cds-NP_461876.3 7.65e-01 100 fucR 6.55e-04 100 gcvA 9.94e-01 100 galR 3.11e-01 100 cds-NP_461929.1 5.47e-05 43_[+1(2.35e-07)]_36 lysR 9.15e-01 100 cds-NP_461937.1 8.18e-01 100 iciA 3.66e-01 100 cds-NP_462000.3 3.03e-01 100 gshB 1.07e-10 24_[+2(2.46e-14)]_38 yqgE 3.42e-01 100 cds-NP_462014.1 9.47e-02 100 cds-NP_462036.1 1.00e+00 100 cca 2.58e-01 100 rpsU 3.08e-01 100 rpoD 5.10e-01 100 yqjI 9.08e-01 100 yhaJ 2.01e-10 7_[+3(1.57e-13)]_45 tdcA 9.44e-01 100 agaR 9.72e-01 100 cds-NP_462175.1 3.56e-01 100 rpsO 2.18e-01 100 infB 5.95e-01 100 nusA 7.98e-01 100 greA 8.76e-16 [+3(7.29e-19)]_52 rpmA 5.47e-01 100 rplU 4.46e-01 100 nlp 8.20e-01 100 yrbA 3.30e-01 100 rpoN 5.83e-01 100 nanK 6.29e-07 23_[+1(2.12e-08)]_56 yhcK 5.00e-01 100 rpsI 2.67e-01 100 rplM 9.86e-01 100 cds-NP_462267.1 4.91e-01 100 cds-NP_462268.1 3.26e-01 100 yhcS 9.93e-01 100 prmA 2.87e-01 100 fis 1.68e-01 100 envR 4.42e-01 100 zntR 8.98e-01 100 rplQ 1.40e-01 100 rpoA 9.72e-01 100 rpsD 7.38e-01 100 rpsK 3.52e-01 100 rpsM 8.92e-01 100 rpmJ 1.85e-01 100 rplO 1.63e-01 100 rpmD 1.90e-01 100 rpsE 1.04e-02 100 rplR 4.97e-02 100 rplF 2.40e-13 3_[+3(2.63e-16)]_49 rpsH 6.28e-01 100 rpsN 4.99e-02 100 rplE 5.77e-01 100 rplX 5.98e-01 100 rplN 4.56e-01 100 rpsQ 1.93e-01 100 rpmC 7.20e-01 100 rplP 8.40e-01 100 rpsC 4.90e-01 100 rplV 4.74e-01 100 rpsS 5.59e-01 100 rplB 1.31e-01 100 rplW 7.68e-01 100 rplD 2.35e-01 100 rplC 4.65e-01 100 rpsJ 8.44e-01 100 tufA 8.95e-01 100 fusA 7.26e-01 100 rpsG 9.14e-01 100 rpsL 9.62e-01 100 greB 7.33e-01 100 yhgF 1.39e-01 100 malT 8.17e-12 58_[+2(3.68e-15)]_4 rtcR 8.06e-01 100 glpR 1.17e-02 100 cds-NP_462434.1 3.56e-02 100 gntR 6.08e-01 100 rpoH 2.53e-01 100 nikR 2.96e-03 100 cds-NP_462503.1 6.35e-01 100 yhjC 6.28e-01 100 cds-NP_462535.1 4.08e-01 100 yiaG 3.07e-01 100 yiaJ 7.34e-02 100 cds-NP_462581.1 1.82e-01 100 selB 2.16e-01 100 mtlR 2.67e-07 15_[+1(1.74e-08)]_24_[+1(1.58e-05)]_\ 19 lldR 9.05e-01 100 cds-NP_462596.1 5.67e-01 100 rpmG 1.53e-01 100 rpmB 4.75e-01 100 ttk 5.63e-01 100 cds-NP_462636.1 3.41e-01 100 rpoZ 7.57e-01 100 cds-NP_462672.1 4.06e-01 100 cds-NP_462677.1 7.84e-01 100 cds-NP_462684.1 3.75e-01 100 cds-NP_462693.1 3.11e-01 100 dsdC 1.61e-01 100 dgoR 7.50e-01 100 cds-NP_462734.1 5.74e-01 100 dnaN 7.45e-01 100 yidZ 1.73e-02 100 atpC 3.25e-01 100 atpD 2.74e-05 50_[+1(6.80e-09)]_29 atpG 3.65e-01 100 atpA 2.76e-03 100 atpH 8.19e-01 100 atpF 4.10e-01 100 atpE 8.65e-10 1_[+3(1.34e-13)]_51 atpB 6.07e-14 9_[+3(8.83e-18)]_43 atpI 2.20e-01 100 asnC 9.56e-01 100 rbsR 5.79e-12 31_[+2(6.93e-15)]_31 yieP 4.49e-01 100 yifA 6.69e-01 100 ilvY 4.08e-01 100 rho 3.45e-01 100 metR 2.39e-01 100 rfaH 7.41e-01 100 polA 2.74e-01 100 yihW 4.82e-01 100 cds-NP_462910.3 9.92e-01 100 cds-NP_462913.3 5.32e-02 100 cds-NP_462923.1 9.71e-01 100 cds-NP_462949.1 1.97e-05 64_[+1(1.79e-07)]_15 ydeW 4.75e-01 100 cytR 1.23e-02 13_[+3(4.19e-05)]_39 rpmE 3.51e-01 100 metJ 1.53e-01 100 oxyR 4.81e-01 100 tufB 4.37e-01 100 nusG 2.94e-01 100 rplK 2.48e-02 38_[+2(2.43e-05)]_24 rplA 4.66e-11 4_[+2(3.99e-14)]_58 rplJ 5.35e-01 100 rplL 7.71e-01 100 rpoB 7.28e-02 100 rpoC 6.10e-02 100 iclR 9.99e-01 100 lexA 1.00e+00 100 soxR 6.97e-01 100 cds-NP_463135.1 6.34e-01 100 cds-NP_463185.1 3.43e-01 100 efp 4.53e-01 100 yjeB 9.55e-01 100 yjfQ 9.82e-01 100 rpsF 8.62e-05 46_[+1(9.95e-08)]_33 rpsR 7.87e-01 100 rplI 1.29e-02 100 ytfH 8.11e-01 100 ytfJ 6.85e-01 100 cds-NP_463278.1 9.99e-01 100 cds-NP_463309.1 5.22e-02 100 cds-NP_463311.1 3.73e-01 100 treR 2.83e-01 100 yjgF 2.91e-01 100 holC 6.82e-03 58_[+1(4.34e-05)]_21 idnR 5.92e-02 100 uxuR 4.44e-01 100 yjiE 2.81e-01 100 cds-NP_463393.1 1.28e-01 100 holD 2.98e-01 100 cds-NP_490539.1 2.18e-01 100 samB_2 4.05e-01 100 samA 2.05e-01 100 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (3) found. ******************************************************************************** CPU: kodomo ********************************************************************************