******************************************************************************** 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 ------------- ------ ------ ------------- ------ ------ nhaR 1.0000 100 rpsT 1.0000 100 polB 1.0000 100 leuO 1.0000 100 cra 1.0000 100 pdhR 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 dinB 1.0000 100 perR 1.0000 100 xynR 1.0000 100 yagP 1.0000 100 ykgO 1.0000 100 ykgM 1.0000 100 betI 1.0000 100 yahB 1.0000 100 prpR 1.0000 100 cynR 1.0000 100 lacI 1.0000 100 mhpR 1.0000 100 yaiX 1.0000 100 yaiX_2 1.0000 100 mak 1.0000 100 nrdR 1.0000 100 nusB 1.0000 100 decR 1.0000 100 acrR 1.0000 100 dnaX 1.0000 100 dnaX_2 1.0000 100 cueR 1.0000 100 allS 1.0000 100 allR 1.0000 100 entF 1.0000 100 ybdO 1.0000 100 rnk 1.0000 100 ybeF 1.0000 100 holA 1.0000 100 nagC 1.0000 100 mngR 1.0000 100 ybhD 1.0000 100 cecR 1.0000 100 mntR 1.0000 100 deoR 1.0000 100 rimK 1.0000 100 infA 1.0000 100 lrp 1.0000 100 ycaN 1.0000 100 rpsA 1.0000 100 rutC 1.0000 100 rutR 1.0000 100 rimJ 1.0000 100 rpmF 1.0000 100 holB 1.0000 100 comR 1.0000 100 mfd 1.0000 100 nagK 1.0000 100 ymfK 1.0000 100 bluR 1.0000 100 umuD 1.0000 100 umuC 1.0000 100 fadR 1.0000 100 dhaR 1.0000 100 ychF 1.0000 100 yciO 1.0000 100 cysB 1.0000 100 yciH 1.0000 100 yciT 1.0000 100 puuR 1.0000 100 pspF 1.0000 100 pspC 1.0000 100 ycjW 1.0000 100 tyrR 1.0000 100 pgrR 1.0000 100 abgR 1.0000 100 paaX 1.0000 100 ydcI 1.0000 100 rimL 1.0000 100 sutR 1.0000 100 ydcR 1.0000 100 mcbR 1.0000 100 lsrR 1.0000 100 yneJ 1.0000 100 marR 1.0000 100 rspR 1.0000 100 relE 1.0000 100 dicA 1.0000 100 speG 1.0000 100 mlc 1.0000 100 ynfL 1.0000 100 uidR 1.0000 100 malI 1.0000 100 slyA 1.0000 100 nemR 1.0000 100 rnt 1.0000 100 purR 1.0000 100 punR 1.0000 100 rplT 1.0000 100 rpmI 1.0000 100 infC 1.0000 100 ydjF 1.0000 100 dmlR 1.0000 100 yoaB 1.0000 100 kdgR 1.0000 100 exoX 1.0000 100 yebK 1.0000 100 fliA 1.0000 100 cbl 1.0000 100 nac 1.0000 100 yeeY 1.0000 100 gatR 1.0000 100 yegW 1.0000 100 galS 1.0000 100 yeiE 1.0000 100 yeiP 1.0000 100 rplY 1.0000 100 yfaX 1.0000 100 lrhA 1.0000 100 torI 1.0000 100 dsdC 1.0000 100 yfeD 1.0000 100 xapR 1.0000 100 yfeR 1.0000 100 murR 1.0000 100 hyfR 1.0000 100 iscR 1.0000 100 csiE 1.0000 100 hcaR 1.0000 100 yphH 1.0000 100 yfhH 1.0000 100 rpoE 1.0000 100 yfiE 1.0000 100 rplS 1.0000 100 rpsP 1.0000 100 alpA 1.0000 100 yfjR 1.0000 100 glaR 1.0000 100 ygaV 1.0000 100 mprA 1.0000 100 srlR 1.0000 100 norR 1.0000 100 ascG 1.0000 100 fhlA 1.0000 100 ygbI 1.0000 100 rpoS 1.0000 100 fucR 1.0000 100 gcvA 1.0000 100 galR 1.0000 100 lysR 1.0000 100 ygeV 1.0000 100 argP 1.0000 100 ygfI 1.0000 100 fumE 1.0000 100 gshB 1.0000 100 yqgE 1.0000 100 glcC 1.0000 100 mqsA 1.0000 100 cca 1.0000 100 ttdR 1.0000 100 rpsU 1.0000 100 rpoD 1.0000 100 nfeR 1.0000 100 ebgR 1.0000 100 higA 1.0000 100 exuR 1.0000 100 yhaJ 1.0000 100 tdcF 1.0000 100 tdcA 1.0000 100 agaR 1.0000 100 rpsO 1.0000 100 infB 1.0000 100 infB_2 1.0000 100 infB_3 1.0000 100 nusA 1.0000 100 greA 1.0000 100 rpmA 1.0000 100 rplU 1.0000 100 sfsB 1.0000 100 ibaG 1.0000 100 rpoN 1.0000 100 nanK 1.0000 100 nanR 1.0000 100 rpsI 1.0000 100 rplM 1.0000 100 aaeR 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 frlR 1.0000 100 greB 1.0000 100 yhgF 1.0000 100 malT 1.0000 100 rtcR 1.0000 100 gntR 1.0000 100 rpoH 1.0000 100 nikR 1.0000 100 arsR 1.0000 100 rcdB 1.0000 100 yiaG 1.0000 100 plaR 1.0000 100 yiaU 1.0000 100 selB 1.0000 100 mtlR 1.0000 100 lldR 1.0000 100 rpmG 1.0000 100 rpmB 1.0000 100 slmA 1.0000 100 rpoZ 1.0000 100 yidP 1.0000 100 dgoR 1.0000 100 dnaN 1.0000 100 yidZ 1.0000 100 bglG 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 hdfR 1.0000 100 ilvY 1.0000 100 rho 1.0000 100 metR 1.0000 100 rfaH 1.0000 100 polA 1.0000 100 yihL 1.0000 100 csqR 1.0000 100 frvR 1.0000 100 cytR 1.0000 100 rpmE 1.0000 100 metJ 1.0000 100 oxyR 1.0000 100 fabR 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 alsK 1.0000 100 alsR 1.0000 100 phnF 1.0000 100 efp 1.0000 100 nsrR 1.0000 100 ulaR 1.0000 100 rpsF 1.0000 100 rpsR 1.0000 100 rplI 1.0000 100 ytfH 1.0000 100 ytfJ 1.0000 100 treR 1.0000 100 ridA 1.0000 100 yjgH 1.0000 100 bdcR 1.0000 100 holC 1.0000 100 idnR 1.0000 100 fecI 1.0000 100 yjhU 1.0000 100 yjhI 1.0000 100 sgcR 1.0000 100 uxuR 1.0000 100 hypT 1.0000 100 yjiR 1.0000 100 lgoR 1.0000 100 holD 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= 312 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= 31200 N= 312 sample: seed= 0 hsfrac= 0 searchsize= 31200 norand= no csites= 1000 Letter frequencies in dataset: A 0.275 C 0.225 G 0.211 T 0.29 Background letter frequencies (from file dataset with add-one prior applied): A 0.275 C 0.225 G 0.211 T 0.29 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF GCRYMHKDTGYGCDTYSHGCYTCGMCGWYYTGWYSGCGYTS MEME-1 width = 41 sites = 7 llr = 216 E-value = 8.9e-009 ******************************************************************************** -------------------------------------------------------------------------------- Motif GCRYMHKDTGYGCDTYSHGCYTCGMCGWYYTGWYSGCGYTS MEME-1 Description -------------------------------------------------------------------------------- Simplified A :14:6314::::33:::33:1:::4::41:::3:::::::1 pos.-specific C 19:443::::6:7::644:7419:4a:1463::4417:4:3 probability G 9:41::33:7:7:3114:73:11a::a:1::a1:6937::6 matrix T ::14:463a343:49313::47::1::4347:66:::36a: bits 2.2 * ** * 2.0 * ** * 1.8 * * ** * * 1.6 ** * ** ** * * * Relative 1.3 ** ** * * ** ** ** * *** * Entropy 1.1 ** ***** * ** ** ** *** **** * (44.4 bits) 0.9 ** * ***** * ** ** ** *** ******** 0.7 *** * ***** *** ** *** ** *** ******** 0.4 **************************** ************ 0.2 ***************************************** 0.0 ----------------------------------------- Multilevel GCACATTATGCGCTTCCCGCCTCGACGACCTGTTGGCGTTG consensus GTCAGG TTTAA TGAAGT C TTTC ACC GTC C sequence C T G T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCRYMHKDTGYGCDTYSHGCYTCGMCGWYYTGWYSGCGYTS MEME-1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ----------------------------------------- dnaX_2 8 6.65e-17 ACGGACA GCACAAGATGTGCATTCAGCCTCGCCGTTCTGACGGGGCTG TGTTAGCATT dnaX 8 6.65e-17 ACGGACA GCACAAGATGTGCATTCAGCCTCGCCGTTCTGACGGGGCTG TGTTAGCATT infB_3 16 3.06e-16 TTGCACTCCG GCGTCTTGTTCGATTCGCACTTCGACGACTTGTTCGCTTTG CACTTCGACG infB_2 37 3.06e-16 TTGCACTCCG GCGTCTTGTTCGATTCGCACTTCGACGACTTGTTCGCTTTG CACTTCGACG yidZ 60 2.55e-14 TGAGCCTGTT GCTGATTATGTTCGTCGCGCCTGGACGCCCCGTTGCCGCTC rpsI 31 8.95e-14 ACTTTCAAAT GCGCCCATTGCTCGTGTTGGTGCGCCGTGTCGTTGGCGTTC AAGAACTGTA speG 15 1.10e-12 ACTGGGAGCC CAATACTTTGCGCTGCCTGGACCGTCGAACTGGCCGCGTTA TTACCCCCTA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCRYMHKDTGYGCDTYSHGCYTCGMCGWYYTGWYSGCGYTS MEME-1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- dnaX_2 6.6e-17 7_[+1]_52 dnaX 6.6e-17 7_[+1]_52 infB_3 3.1e-16 15_[+1]_44 infB_2 3.1e-16 36_[+1]_23 yidZ 2.6e-14 59_[+1] rpsI 9e-14 30_[+1]_29 speG 1.1e-12 14_[+1]_45 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCRYMHKDTGYGCDTYSHGCYTCGMCGWYYTGWYSGCGYTS MEME-1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF GCRYMHKDTGYGCDTYSHGCYTCGMCGWYYTGWYSGCGYTS width=41 seqs=7 dnaX_2 ( 8) GCACAAGATGTGCATTCAGCCTCGCCGTTCTGACGGGGCTG 1 dnaX ( 8) GCACAAGATGTGCATTCAGCCTCGCCGTTCTGACGGGGCTG 1 infB_3 ( 16) GCGTCTTGTTCGATTCGCACTTCGACGACTTGTTCGCTTTG 1 infB_2 ( 37) GCGTCTTGTTCGATTCGCACTTCGACGACTTGTTCGCTTTG 1 yidZ ( 60) GCTGATTATGTTCGTCGCGCCTGGACGCCCCGTTGCCGCTC 1 rpsI ( 31) GCGCCCATTGCTCGTGTTGGTGCGCCGTGTCGTTGGCGTTC 1 speG ( 15) CAATACTTTGCGCTGCCTGGACCGTCGAACTGGCCGCGTTA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCRYMHKDTGYGCDTYSHGCYTCGMCGWYYTGWYSGCGYTS MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 41 n= 18720 bayes= 11.2282 E= 8.9e-009 -945 -65 202 -945 -94 193 -945 -945 64 -945 102 -102 -945 93 -56 56 106 93 -945 -945 6 35 -945 56 -94 -945 44 98 64 -945 44 -2 -945 -945 -945 179 -945 -945 176 -2 -945 134 -945 56 -945 -945 176 -2 6 167 -945 -945 6 -945 44 56 -945 -945 -56 156 -945 134 -56 -2 -945 93 102 -102 6 93 -945 -2 6 -945 176 -945 -945 167 44 -945 -94 93 -945 56 -945 -65 -56 130 -945 193 -56 -945 -945 -945 225 -945 64 93 -945 -102 -945 215 -945 -945 -945 -945 225 -945 64 -65 -945 56 -94 93 -56 -2 -945 134 -945 56 -945 35 -945 130 -945 -945 225 -945 6 -945 -56 98 -945 93 -945 98 -945 93 144 -945 -945 -65 202 -945 -945 167 44 -945 -945 -945 176 -2 -945 93 -945 98 -945 -945 -945 179 -94 35 144 -945 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCRYMHKDTGYGCDTYSHGCYTCGMCGWYYTGWYSGCGYTS MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 41 nsites= 7 E= 8.9e-009 0.000000 0.142857 0.857143 0.000000 0.142857 0.857143 0.000000 0.000000 0.428571 0.000000 0.428571 0.142857 0.000000 0.428571 0.142857 0.428571 0.571429 0.428571 0.000000 0.000000 0.285714 0.285714 0.000000 0.428571 0.142857 0.000000 0.285714 0.571429 0.428571 0.000000 0.285714 0.285714 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.714286 0.285714 0.000000 0.571429 0.000000 0.428571 0.000000 0.000000 0.714286 0.285714 0.285714 0.714286 0.000000 0.000000 0.285714 0.000000 0.285714 0.428571 0.000000 0.000000 0.142857 0.857143 0.000000 0.571429 0.142857 0.285714 0.000000 0.428571 0.428571 0.142857 0.285714 0.428571 0.000000 0.285714 0.285714 0.000000 0.714286 0.000000 0.000000 0.714286 0.285714 0.000000 0.142857 0.428571 0.000000 0.428571 0.000000 0.142857 0.142857 0.714286 0.000000 0.857143 0.142857 0.000000 0.000000 0.000000 1.000000 0.000000 0.428571 0.428571 0.000000 0.142857 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.428571 0.142857 0.000000 0.428571 0.142857 0.428571 0.142857 0.285714 0.000000 0.571429 0.000000 0.428571 0.000000 0.285714 0.000000 0.714286 0.000000 0.000000 1.000000 0.000000 0.285714 0.000000 0.142857 0.571429 0.000000 0.428571 0.000000 0.571429 0.000000 0.428571 0.571429 0.000000 0.000000 0.142857 0.857143 0.000000 0.000000 0.714286 0.285714 0.000000 0.000000 0.000000 0.714286 0.285714 0.000000 0.428571 0.000000 0.571429 0.000000 0.000000 0.000000 1.000000 0.142857 0.285714 0.571429 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCRYMHKDTGYGCDTYSHGCYTCGMCGWYYTGWYSGCGYTS MEME-1 regular expression -------------------------------------------------------------------------------- GC[AG][CT][AC][TAC][TG][AGT]T[GT][CT][GT][CA][TAG]T[CT][CG][CAT][GA][CG][CT]TCG[AC]CG[AT][CT][CT][TC]G[TA][TC][GC]G[CG][GT][TC]T[GC] -------------------------------------------------------------------------------- Time 43.38 secs. ******************************************************************************** ******************************************************************************** MOTIF TAGCABTACSCCYKCGTGAHDCCACCTTYYAKCGWDTVAGDGSBTGCCA MEME-2 width = 49 sites = 4 llr = 176 E-value = 1.9e-002 ******************************************************************************** -------------------------------------------------------------------------------- Motif TAGCABTACSCCYKCGTGAHDCCACCTTYYAKCGWDTVAGDGSBTGCCA MEME-2 Description -------------------------------------------------------------------------------- Simplified A :8::8::a::3::::3::a533:8::::::8:::53:3a:5::::333a pos.-specific C :33a:3::a58a5:8:33:3:88:88::55::a::::5::::55::88: probability G ::8:33:::5:::538:8::3:333333::35:8:3:3:83a53:8::: matrix T a::::5a:::::55::8::35:::::8855:5:355a::33::3a:::: bits 2.2 * * * * * 2.0 * * * * * 1.8 * * *** * * * * * * * * 1.6 * * *** * * * * * * * * Relative 1.3 * ** *** ** ** ** ** ** ** * ** * ***** Entropy 1.1 ***** ****** ****** ******* **** * ** ** ***** (63.5 bits) 0.9 ***** ************* ************** * ** ** ***** 0.7 ***** ************* ************** **** ******** 0.4 ************************************************* 0.2 ************************************************* 0.0 ------------------------------------------------- Multilevel TAGCATTACCCCCGCGTGAATCCACCTTCCAGCGATTCAGAGCCTGCCA consensus CC GC GA TTGACC CAAGGGGGGTTGT TTA A TG GG AAA sequence G TG G G T T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TAGCABTACSCCYKCGTGAHDCCACCTTYYAKCGWDTVAGDGSBTGCCA MEME-2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------------------------------------------- dnaX_2 52 3.93e-28 GGGGCTGTGT TAGCATTACCCCTTCGTGAATCCACCTTCCAGCGTTTCAGAGCCTGCCA dnaX 52 3.93e-28 GGGGCTGTGT TAGCATTACCCCTTCGTGAATCCACCTTCCAGCGTTTCAGAGCCTGCCA fucR 49 2.66e-18 CGTAATCTCA TACCGGTACGCCCGCATGACGCGGGCGGTTATCGAATGATGGGGTGAAA AAT gatR 7 3.99e-18 GCCCGG TCGCACTACGACCGGGCCATAACACGTTTTGTCTAGTAAGTGGTTACCA GGGGGAAGCA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TAGCABTACSCCYKCGTGAHDCCACCTTYYAKCGWDTVAGDGSBTGCCA MEME-2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- dnaX_2 3.9e-28 51_[+2] dnaX 3.9e-28 51_[+2] fucR 2.7e-18 48_[+2]_3 gatR 4e-18 6_[+2]_45 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TAGCABTACSCCYKCGTGAHDCCACCTTYYAKCGWDTVAGDGSBTGCCA MEME-2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF TAGCABTACSCCYKCGTGAHDCCACCTTYYAKCGWDTVAGDGSBTGCCA width=49 seqs=4 dnaX_2 ( 52) TAGCATTACCCCTTCGTGAATCCACCTTCCAGCGTTTCAGAGCCTGCCA 1 dnaX ( 52) TAGCATTACCCCTTCGTGAATCCACCTTCCAGCGTTTCAGAGCCTGCCA 1 fucR ( 49) TACCGGTACGCCCGCATGACGCGGGCGGTTATCGAATGATGGGGTGAAA 1 gatR ( 7) TCGCACTACGACCGGGCCATAACACGTTTTGTCTAGTAAGTGGTTACCA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TAGCABTACSCCYKCGTGAHDCCACCTTYYAKCGWDTVAGDGSBTGCCA MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 49 n= 16224 bayes= 11.9855 E= 1.9e-002 -865 -865 -865 178 145 15 -865 -865 -865 15 183 -865 -865 215 -865 -865 145 -865 25 -865 -865 15 25 79 -865 -865 -865 178 186 -865 -865 -865 -865 215 -865 -865 -865 115 124 -865 -14 174 -865 -865 -865 215 -865 -865 -865 115 -865 79 -865 -865 124 79 -865 174 25 -865 -14 -865 183 -865 -865 15 -865 137 -865 15 183 -865 186 -865 -865 -865 86 15 -865 -21 -14 -865 25 79 -14 174 -865 -865 -865 174 25 -865 145 -865 25 -865 -865 174 25 -865 -865 174 25 -865 -865 -865 25 137 -865 -865 25 137 -865 115 -865 79 -865 115 -865 79 145 -865 25 -865 -865 -865 124 79 -865 215 -865 -865 -865 -865 183 -21 86 -865 -865 79 -14 -865 25 79 -865 -865 -865 178 -14 115 25 -865 186 -865 -865 -865 -865 -865 183 -21 86 -865 25 -21 -865 -865 224 -865 -865 115 124 -865 -865 115 25 -21 -865 -865 -865 178 -14 -865 183 -865 -14 174 -865 -865 -14 174 -865 -865 186 -865 -865 -865 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TAGCABTACSCCYKCGTGAHDCCACCTTYYAKCGWDTVAGDGSBTGCCA MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 49 nsites= 4 E= 1.9e-002 0.000000 0.000000 0.000000 1.000000 0.750000 0.250000 0.000000 0.000000 0.000000 0.250000 0.750000 0.000000 0.000000 1.000000 0.000000 0.000000 0.750000 0.000000 0.250000 0.000000 0.000000 0.250000 0.250000 0.500000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.500000 0.500000 0.000000 0.250000 0.750000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.500000 0.000000 0.500000 0.000000 0.000000 0.500000 0.500000 0.000000 0.750000 0.250000 0.000000 0.250000 0.000000 0.750000 0.000000 0.000000 0.250000 0.000000 0.750000 0.000000 0.250000 0.750000 0.000000 1.000000 0.000000 0.000000 0.000000 0.500000 0.250000 0.000000 0.250000 0.250000 0.000000 0.250000 0.500000 0.250000 0.750000 0.000000 0.000000 0.000000 0.750000 0.250000 0.000000 0.750000 0.000000 0.250000 0.000000 0.000000 0.750000 0.250000 0.000000 0.000000 0.750000 0.250000 0.000000 0.000000 0.000000 0.250000 0.750000 0.000000 0.000000 0.250000 0.750000 0.000000 0.500000 0.000000 0.500000 0.000000 0.500000 0.000000 0.500000 0.750000 0.000000 0.250000 0.000000 0.000000 0.000000 0.500000 0.500000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.750000 0.250000 0.500000 0.000000 0.000000 0.500000 0.250000 0.000000 0.250000 0.500000 0.000000 0.000000 0.000000 1.000000 0.250000 0.500000 0.250000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.750000 0.250000 0.500000 0.000000 0.250000 0.250000 0.000000 0.000000 1.000000 0.000000 0.000000 0.500000 0.500000 0.000000 0.000000 0.500000 0.250000 0.250000 0.000000 0.000000 0.000000 1.000000 0.250000 0.000000 0.750000 0.000000 0.250000 0.750000 0.000000 0.000000 0.250000 0.750000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TAGCABTACSCCYKCGTGAHDCCACCTTYYAKCGWDTVAGDGSBTGCCA MEME-2 regular expression -------------------------------------------------------------------------------- T[AC][GC]C[AG][TCG]TAC[CG][CA]C[CT][GT][CG][GA][TC][GC]A[ACT][TAG][CA][CG][AG][CG][CG][TG][TG][CT][CT][AG][GT]C[GT][AT][TAG]T[CAG]A[GT][AGT]G[CG][CGT]T[GA][CA][CA]A -------------------------------------------------------------------------------- Time 84.06 secs. ******************************************************************************** ******************************************************************************** MOTIF WTSGACRCCTYTTTCWSTTT MEME-3 width = 20 sites = 6 llr = 122 E-value = 1.3e-001 ******************************************************************************** -------------------------------------------------------------------------------- Motif WTSGACRCCTYTTTCWSTTT MEME-3 Description -------------------------------------------------------------------------------- Simplified A 3::28:3:::::2::5:::: pos.-specific C ::5:2a2aa:3:::a:3::: probability G ::38::5::::::::27::2 matrix T 7a2::::::a7a8a:3:aa8 bits 2.2 * ** * 2.0 * ** * 1.8 * * *** * ** ** 1.6 * * * *** * ** ** Relative 1.3 * *** *** * ** *** Entropy 1.1 * *** *** **** **** (29.4 bits) 0.9 ** *** ******** **** 0.7 *************** **** 0.4 ******************** 0.2 ******************** 0.0 -------------------- Multilevel TTCGACGCCTTTTTCAGTTT consensus A G A C TC sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif WTSGACRCCTYTTTCWSTTT MEME-3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------------------- infB_3 60 6.49e-12 CGCTTTGCAC TTCGACGCCTTTTTCTGTTT CACTCGTTAG infB_2 81 6.49e-12 CGCTTTGCAC TTCGACGCCTTTTTCTGTTT atpC 52 6.33e-11 AGGTAGCTTC TTCGACACCTTTTTCGGTTT TTTGAAATTG frvR 52 8.92e-10 GACTGCTGGA ATTGACGCCTCTTTCAGTTG CGCAAATCGG tsf 30 1.42e-09 GGGCCTGCAT ATGGCCCCCTTTTTCACTTT TATATCTGTG relE 31 2.76e-09 CTTCTACGAC TTGAACACCTCTATCACTTT CTTGCCGAAG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif WTSGACRCCTYTTTCWSTTT MEME-3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- infB_3 6.5e-12 59_[+3]_21 infB_2 6.5e-12 80_[+3] atpC 6.3e-11 51_[+3]_29 frvR 8.9e-10 51_[+3]_29 tsf 1.4e-09 29_[+3]_51 relE 2.8e-09 30_[+3]_50 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif WTSGACRCCTYTTTCWSTTT MEME-3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF WTSGACRCCTYTTTCWSTTT width=20 seqs=6 infB_3 ( 60) TTCGACGCCTTTTTCTGTTT 1 infB_2 ( 81) TTCGACGCCTTTTTCTGTTT 1 atpC ( 52) TTCGACACCTTTTTCGGTTT 1 frvR ( 52) ATTGACGCCTCTTTCAGTTG 1 tsf ( 30) ATGGCCCCCTTTTTCACTTT 1 relE ( 31) TTGAACACCTCTATCACTTT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif WTSGACRCCTYTTTCWSTTT MEME-3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 20 n= 25272 bayes= 12.4875 E= 1.3e-001 28 -923 -923 120 -923 -923 -923 179 -923 115 66 -80 -72 -923 198 -923 160 -43 -923 -923 -923 215 -923 -923 28 -43 125 -923 -923 215 -923 -923 -923 215 -923 -923 -923 -923 -923 179 -923 57 -923 120 -923 -923 -923 179 -72 -923 -923 152 -923 -923 -923 179 -923 215 -923 -923 86 -923 -34 20 -923 57 166 -923 -923 -923 -923 179 -923 -923 -923 179 -923 -923 -34 152 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif WTSGACRCCTYTTTCWSTTT MEME-3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 20 nsites= 6 E= 1.3e-001 0.333333 0.000000 0.000000 0.666667 0.000000 0.000000 0.000000 1.000000 0.000000 0.500000 0.333333 0.166667 0.166667 0.000000 0.833333 0.000000 0.833333 0.166667 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.333333 0.166667 0.500000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.333333 0.000000 0.666667 0.000000 0.000000 0.000000 1.000000 0.166667 0.000000 0.000000 0.833333 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.500000 0.000000 0.166667 0.333333 0.000000 0.333333 0.666667 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.166667 0.833333 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif WTSGACRCCTYTTTCWSTTT MEME-3 regular expression -------------------------------------------------------------------------------- [TA]T[CG]GAC[GA]CCT[TC]TTTC[AT][GC]TTT -------------------------------------------------------------------------------- Time 124.44 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- nhaR 2.62e-01 100 rpsT 8.51e-01 100 polB 6.38e-01 100 leuO 9.22e-01 100 cra 7.95e-01 100 pdhR 2.84e-01 100 pcnB 1.34e-01 100 rpsB 3.82e-01 100 tsf 2.01e-06 29_[+3(1.42e-09)]_51 dnaE 4.49e-01 100 rof 2.01e-01 100 yafC 4.42e-01 100 dnaQ 5.49e-01 100 dinB 9.37e-01 100 perR 2.75e-01 100 xynR 8.93e-01 100 yagP 2.33e-01 100 ykgO 8.19e-01 100 ykgM 5.86e-01 100 betI 1.40e-01 100 yahB 6.26e-02 100 prpR 3.04e-01 100 cynR 3.13e-01 100 lacI 2.94e-01 100 mhpR 9.26e-02 100 yaiX 9.07e-01 100 yaiX_2 1.00e+00 100 mak 1.50e-02 100 nrdR 2.95e-01 100 nusB 6.17e-01 100 decR 3.55e-01 100 acrR 4.72e-01 100 dnaX 2.46e-37 7_[+1(6.65e-17)]_3_[+2(3.93e-28)] dnaX_2 2.46e-37 7_[+1(6.65e-17)]_3_[+2(3.93e-28)] cueR 9.21e-02 100 allS 3.67e-01 100 allR 8.41e-01 100 entF 5.11e-01 100 ybdO 5.14e-01 100 rnk 9.41e-01 100 ybeF 8.79e-01 100 holA 8.32e-02 100 nagC 3.35e-02 58_[+1(6.77e-05)]_1 mngR 8.44e-01 100 ybhD 8.34e-01 100 cecR 4.42e-01 100 mntR 8.26e-01 100 deoR 3.08e-01 100 rimK 5.64e-01 100 infA 6.56e-01 100 lrp 9.44e-01 100 ycaN 3.90e-01 100 rpsA 9.63e-01 100 rutC 9.80e-01 100 rutR 3.83e-01 100 rimJ 5.00e-01 100 rpmF 2.46e-01 100 holB 6.29e-01 100 comR 9.98e-01 100 mfd 7.99e-01 100 nagK 6.49e-01 100 ymfK 5.75e-01 100 bluR 9.44e-01 100 umuD 3.38e-01 100 umuC 2.39e-01 100 fadR 7.92e-03 3_[+3(6.66e-05)]_77 dhaR 2.27e-01 100 ychF 8.96e-01 100 yciO 1.35e-02 100 cysB 2.03e-01 100 yciH 8.16e-02 100 yciT 1.00e+00 100 puuR 4.71e-02 100 pspF 5.26e-01 100 pspC 8.45e-02 100 ycjW 4.36e-01 100 tyrR 4.47e-01 100 pgrR 7.52e-01 100 abgR 7.02e-01 100 paaX 6.82e-01 100 ydcI 3.32e-01 100 rimL 3.14e-01 100 sutR 5.84e-01 100 ydcR 9.91e-01 100 mcbR 4.04e-01 100 lsrR 3.50e-01 100 yneJ 9.03e-01 100 marR 4.71e-01 100 rspR 4.11e-01 100 relE 3.75e-06 30_[+3(2.76e-09)]_50 dicA 4.56e-01 100 speG 3.28e-09 14_[+1(1.10e-12)]_45 mlc 4.30e-01 100 ynfL 7.12e-01 100 uidR 8.47e-01 100 malI 3.22e-01 100 slyA 3.92e-01 100 nemR 9.93e-01 100 rnt 8.15e-01 100 purR 8.52e-01 100 punR 7.50e-01 100 rplT 3.67e-01 100 rpmI 9.80e-01 100 infC 6.77e-02 100 ydjF 3.48e-01 100 dmlR 9.76e-02 100 yoaB 3.09e-01 100 kdgR 4.15e-01 100 exoX 1.77e-01 100 yebK 4.57e-01 100 fliA 1.54e-01 100 cbl 9.16e-02 100 nac 4.24e-01 100 yeeY 1.65e-01 100 gatR 5.61e-14 6_[+2(3.99e-18)]_45 yegW 4.96e-01 100 galS 8.98e-01 100 yeiE 3.45e-01 100 yeiP 3.33e-01 100 rplY 1.57e-01 100 yfaX 5.86e-01 100 lrhA 8.20e-01 100 torI 2.06e-01 100 dsdC 2.71e-01 100 yfeD 5.78e-01 100 xapR 6.27e-01 100 yfeR 9.45e-01 100 murR 2.18e-01 100 hyfR 4.40e-01 100 iscR 8.37e-01 100 csiE 9.56e-01 100 hcaR 2.22e-02 100 yphH 9.67e-01 100 yfhH 5.11e-01 100 rpoE 7.25e-01 100 yfiE 6.61e-01 100 rplS 1.52e-02 100 rpsP 9.39e-01 100 alpA 4.78e-01 100 yfjR 5.11e-01 100 glaR 5.13e-01 100 ygaV 9.28e-01 100 mprA 8.55e-01 100 srlR 1.37e-01 100 norR 8.74e-01 100 ascG 2.12e-01 100 fhlA 5.11e-01 100 ygbI 1.43e-03 100 rpoS 6.45e-01 100 fucR 2.04e-15 48_[+2(2.66e-18)]_3 gcvA 2.11e-01 100 galR 5.17e-02 23_[+2(4.72e-05)]_28 lysR 9.51e-01 100 ygeV 6.99e-01 100 argP 9.41e-01 100 ygfI 9.88e-01 100 fumE 4.70e-01 100 gshB 1.22e-01 100 yqgE 1.99e-01 100 glcC 1.93e-01 100 mqsA 7.33e-01 100 cca 3.55e-01 100 ttdR 6.59e-01 100 rpsU 6.61e-01 100 rpoD 9.80e-01 100 nfeR 4.60e-01 100 ebgR 9.08e-01 100 higA 6.71e-01 100 exuR 9.81e-01 100 yhaJ 2.42e-01 100 tdcF 9.76e-01 100 tdcA 9.90e-01 100 agaR 5.28e-02 100 rpsO 2.27e-01 100 infB 2.00e-01 100 infB_2 1.06e-20 36_[+1(3.06e-16)]_3_[+3(6.49e-12)] infB_3 2.53e-21 15_[+1(3.06e-16)]_3_[+3(6.49e-12)]_\ 21 nusA 3.10e-01 100 greA 6.44e-02 100 rpmA 2.62e-01 100 rplU 7.85e-01 100 sfsB 6.41e-01 100 ibaG 9.82e-01 100 rpoN 9.75e-01 100 nanK 6.17e-01 100 nanR 2.51e-01 100 rpsI 1.46e-10 30_[+1(8.95e-14)]_29 rplM 4.27e-01 100 aaeR 8.41e-01 100 prmA 5.61e-01 100 fis 7.08e-01 100 envR 9.69e-01 100 zntR 3.71e-01 100 rplQ 8.75e-02 100 rpoA 2.83e-01 100 rpsD 1.87e-01 100 rpsK 8.13e-01 100 rpsM 6.05e-01 100 rpmJ 2.73e-03 100 rplO 9.09e-01 100 rpmD 4.47e-01 100 rpsE 8.89e-01 100 rplR 3.93e-01 100 rplF 1.72e-01 100 rpsH 9.52e-01 100 rpsN 7.89e-01 100 rplE 3.24e-02 100 rplX 4.87e-01 100 rplN 9.61e-01 100 rpsQ 4.18e-01 100 rpmC 4.25e-02 100 rplP 2.09e-02 100 rpsC 1.11e-01 100 rplV 2.47e-01 100 rpsS 2.30e-02 10_[+1(5.74e-05)]_49 rplB 4.77e-01 100 rplW 6.99e-01 100 rplD 6.38e-02 100 rplC 2.62e-01 100 rpsJ 9.89e-01 100 tufA 1.87e-01 100 fusA 8.26e-01 100 rpsG 6.86e-01 100 rpsL 6.82e-01 100 frlR 4.08e-01 100 greB 9.51e-01 100 yhgF 2.20e-01 100 malT 8.23e-01 100 rtcR 8.03e-01 100 gntR 8.80e-01 100 rpoH 4.72e-01 100 nikR 4.47e-01 100 arsR 3.11e-01 100 rcdB 7.15e-01 100 yiaG 1.34e-01 100 plaR 6.87e-03 43_[+3(1.97e-05)]_37 yiaU 9.03e-01 100 selB 6.92e-01 100 mtlR 4.01e-01 100 lldR 7.87e-01 100 rpmG 6.36e-02 100 rpmB 7.25e-01 100 slmA 2.46e-01 100 rpoZ 5.11e-01 100 yidP 6.53e-01 100 dgoR 3.80e-01 100 dnaN 5.19e-01 100 yidZ 1.38e-10 59_[+1(2.55e-14)] bglG 3.68e-01 100 atpC 1.38e-07 51_[+3(6.33e-11)]_29 atpD 9.31e-01 100 atpG 5.51e-01 100 atpA 6.77e-01 100 atpH 3.91e-01 100 atpF 3.71e-01 100 atpE 5.75e-01 100 atpB 2.57e-01 100 atpI 3.38e-01 100 asnC 6.08e-01 100 rbsR 3.01e-01 100 yieP 1.18e-01 100 hdfR 4.01e-01 100 ilvY 5.81e-02 100 rho 9.42e-01 100 metR 9.88e-01 100 rfaH 1.33e-01 100 polA 4.64e-01 100 yihL 6.11e-01 100 csqR 7.96e-01 100 frvR 7.06e-07 51_[+3(8.92e-10)]_29 cytR 8.50e-01 100 rpmE 1.02e-01 100 metJ 9.36e-01 100 oxyR 3.86e-01 100 fabR 8.12e-01 100 tufB 7.25e-02 100 nusG 7.42e-02 100 rplK 8.28e-02 100 rplA 5.20e-01 100 rplJ 1.75e-01 100 rplL 2.25e-01 100 rpoB 5.01e-01 100 rpoC 1.61e-01 100 iclR 3.98e-01 100 lexA 2.22e-01 100 soxR 2.66e-01 100 alsK 4.14e-03 30_[+1(7.46e-05)]_29 alsR 7.88e-01 100 phnF 1.69e-01 100 efp 5.18e-01 100 nsrR 1.18e-01 100 ulaR 4.52e-01 100 rpsF 1.60e-01 100 rpsR 9.25e-01 100 rplI 4.72e-01 100 ytfH 2.92e-01 100 ytfJ 1.75e-01 100 treR 9.85e-01 100 ridA 3.88e-01 100 yjgH 3.34e-01 100 bdcR 4.31e-01 100 holC 6.22e-01 100 idnR 1.26e-01 100 fecI 7.27e-01 100 yjhU 4.61e-01 100 yjhI 1.56e-01 100 sgcR 1.93e-01 100 uxuR 1.93e-01 100 hypT 3.90e-01 100 yjiR 9.19e-01 100 lgoR 1.76e-01 100 holD 3.08e-01 100 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (3) found. ******************************************************************************** CPU: kodomo ********************************************************************************