******************************************************************************** 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 fruR 1.0000 100 pdhR 1.0000 100 pcnB 1.0000 100 rpsB 1.0000 100 tsf 1.0000 100 dnaE 1.0000 100 yaeO 1.0000 100 yafC 1.0000 100 dnaQ 1.0000 100 dinP 1.0000 100 yajF 1.0000 100 nrdR 1.0000 100 nusB 1.0000 100 ybaO 1.0000 100 acrR 1.0000 100 dnaX 1.0000 100 ybbI 1.0000 100 ybbS 1.0000 100 ybbU 1.0000 100 entF 1.0000 100 cds-NP_706461.1 1.0000 100 rnk 1.0000 100 farR 1.0000 100 nagC 1.0000 100 holA 1.0000 100 ybiH 1.0000 100 cds-NP_706694.1 1.0000 100 deoR 1.0000 100 rimK 1.0000 100 infA 1.0000 100 lrp 1.0000 100 cds-NP_706797.1 1.0000 100 cds-NP_706801.1 1.0000 100 rpsA 1.0000 100 cds-NP_706932.1 1.0000 100 ycdC 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 umuD 1.0000 100 umuC 1.0000 100 fadR 1.0000 100 cds-NP_707110.1 1.0000 100 ychF 1.0000 100 yciO 1.0000 100 cysB 1.0000 100 yciH 1.0000 100 cds-NP_707193.1 1.0000 100 ycjC 1.0000 100 pspF 1.0000 100 pspC 1.0000 100 ycjW 1.0000 100 tyrR 1.0000 100 cds-NP_707242.1 1.0000 100 cds-NP_707292.1 1.0000 100 cds-NP_707313.1 1.0000 100 cds-NP_707343.1 1.0000 100 infC 1.0000 100 rpmI 1.0000 100 rplT 1.0000 100 relE 1.0000 100 marR 1.0000 100 ydeW 1.0000 100 mlc 1.0000 100 ynfL 1.0000 100 uidR 1.0000 100 malI 1.0000 100 slyA 1.0000 100 cds-NP_707550.2 1.0000 100 rnt 1.0000 100 ydhB 1.0000 100 cds-NP_707629.1 1.0000 100 cds-NP_707644.1 1.0000 100 rimL 1.0000 100 cds-NP_707650.1 1.0000 100 cds-NP_707706.2 1.0000 100 yebK 1.0000 100 cds-NP_707754.1 1.0000 100 cbl 1.0000 100 nac 1.0000 100 yeeY 1.0000 100 gatR 1.0000 100 galS 1.0000 100 yeiE 1.0000 100 yeiP 1.0000 100 rplY 1.0000 100 lrhA 1.0000 100 cds-NP_708235.2 1.0000 100 yfeD 1.0000 100 yfeR 1.0000 100 yfeT 1.0000 100 cds-NP_708290.1 1.0000 100 cds-NP_708370.1 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 ygaE 1.0000 100 cds-NP_708481.1 1.0000 100 srlR 1.0000 100 ygaA 1.0000 100 ascG 1.0000 100 fhlA 1.0000 100 ygbI 1.0000 100 cds-NP_708541.1 1.0000 100 cds-NP_708545.1 1.0000 100 cds-NP_708546.1 1.0000 100 fucR 1.0000 100 gcvA 1.0000 100 galR 1.0000 100 lysR 1.0000 100 iciA 1.0000 100 ygfI 1.0000 100 yggD 1.0000 100 gshB 1.0000 100 yqgE 1.0000 100 cds-NP_708761.1 1.0000 100 glcC 1.0000 100 cds-NP_708799.2 1.0000 100 cca 1.0000 100 ygiP 1.0000 100 rpsU 1.0000 100 rpoD 1.0000 100 yqjI 1.0000 100 ebgR 1.0000 100 ygjM 1.0000 100 exuR 1.0000 100 yhaJ 1.0000 100 yhaR 1.0000 100 tdcA 1.0000 100 agaR 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 yhcI 1.0000 100 yhcK 1.0000 100 rpsI 1.0000 100 rplM 1.0000 100 yhcS 1.0000 100 prmA 1.0000 100 fis 1.0000 100 yrdC 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 tuf 1.0000 100 fusA 1.0000 100 rpsG 1.0000 100 rpsL 1.0000 100 yhfR 1.0000 100 greB 1.0000 100 yhgF 1.0000 100 rtcR 1.0000 100 glpR 1.0000 100 gntR 1.0000 100 rpoH 1.0000 100 yhhG 1.0000 100 cds-NP_709283.2 1.0000 100 yhjC 1.0000 100 yiaJ 1.0000 100 selB 1.0000 100 mtlR 1.0000 100 lldR 1.0000 100 rpmG 1.0000 100 rpmB 1.0000 100 ttk 1.0000 100 rpoZ 1.0000 100 bglG 1.0000 100 dnaN 1.0000 100 yidW 1.0000 100 yidP 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_2 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 yihL 1.0000 100 yihW 1.0000 100 cytR 1.0000 100 rpmE 1.0000 100 metJ 1.0000 100 oxyR 1.0000 100 yijC 1.0000 100 tuf_2 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 sorC 1.0000 100 soxR 1.0000 100 lexA 1.0000 100 yjiE 1.0000 100 uxuR 1.0000 100 cds-NP_709929.2 1.0000 100 holC 1.0000 100 yjgJ 1.0000 100 yjgH 1.0000 100 yjgF 1.0000 100 treR 1.0000 100 ytfJ 1.0000 100 ytfH 1.0000 100 ytfA 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 hpcR 1.0000 100 yjjM 1.0000 100 holD 1.0000 100 cds-NP_710125.1 1.0000 100 ******************************************************************************** ******************************************************************************** COMMAND LINE SUMMARY ******************************************************************************** This information can also be useful in the event you wish to report a problem with the MEME software. command: meme housekeeping.fasta -dna -nmotifs 3 -minw 6 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 0.273 C 0.23 G 0.215 T 0.282 Background letter frequencies (from file dataset with add-one prior applied): A 0.273 C 0.23 G 0.215 T 0.282 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF GCCAMGCAABVAMCBYAAAAHCACCABCATVMACTAAATCASYDWGTTSG MEME-1 width = 50 sites = 4 llr = 176 E-value = 1.2e-001 ******************************************************************************** -------------------------------------------------------------------------------- Motif GCCAMGCAABVAMCBYAAAAHCACCABCATVMACTAAATCASYDWGTTSG MEME-1 Description -------------------------------------------------------------------------------- Simplified A :3:85::88:385:::aaa83:8::8::a:55a::88a::8::55::::: pos.-specific C 38a:5:a3:3535a35::::38388:38:335:8:3:::8:55::3:35: probability G 8::::a::353:::3::::3:::33:33::3::3:::::335:3:83:5a matrix T :::3:::::3::::55::::53:::35::8::::a:3:a:::535:88:: bits 2.2 * ** * * 2.0 * ** * * 1.8 * ** * *** * * * ** * 1.6 * ** * *** * * * ** * Relative 1.3 *** ** * *** * ** ** *** *** * * Entropy 1.1 **** **** * * **** ***** *** ********** ***** (63.6 bits) 0.9 ********* *** ***** ***** *** ************ ****** 0.7 ************** ***** ***** *** ************ ****** 0.4 ************************************************** 0.2 ************************************************** 0.0 -------------------------------------------------- Multilevel GCCAAGCAAGCAACTCAAAATCACCATCATAAACTAAATCACCAAGTTCG consensus CA TC CGCACC CT GATCGGTCG CCC G CT GGGTGTCGCG sequence TG G C G G T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCCAMGCAABVAMCBYAAAAHCACCABCATVMACTAAATCASYDWGTTSG MEME-1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------------------------------------------------- cds-NP_709929.2 2 1.44e-28 A GCCACGCAAGCACCTTAAAATCACCATCATACACTAAATCAGTAAGTTGG CAGCATTACC cds-NP_709283.2 26 1.44e-28 GGAAATGGAA GCCACGCAAGCACCTTAAAATCACCATCATACACTAAATCAGTAAGTTGG CAGCATTACC atpB 21 2.22e-18 TAAGAACGGC GACTAGCAATGCACCCAAAACCACGACCACCAAGTCTATGACCGTGGCCG ACATTAATTG cca 1 2.89e-18 . CCCAAGCCGCAAACGCAAAGATCGCTGGATGAACTAAATCGCCTTCTTCG TTGCACTGTC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCCAMGCAABVAMCBYAAAAHCACCABCATVMACTAAATCASYDWGTTSG MEME-1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- cds-NP_709929.2 1.4e-28 1_[+1]_49 cds-NP_709283.2 1.4e-28 25_[+1]_25 atpB 2.2e-18 20_[+1]_30 cca 2.9e-18 [+1]_50 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCCAMGCAABVAMCBYAAAAHCACCABCATVMACTAAATCASYDWGTTSG MEME-1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF GCCAMGCAABVAMCBYAAAAHCACCABCATVMACTAAATCASYDWGTTSG width=50 seqs=4 cds-NP_709929.2 ( 2) GCCACGCAAGCACCTTAAAATCACCATCATACACTAAATCAGTAAGTTGG 1 cds-NP_709283.2 ( 26) GCCACGCAAGCACCTTAAAATCACCATCATACACTAAATCAGTAAGTTGG 1 atpB ( 21) GACTAGCAATGCACCCAAAACCACGACCACCAAGTCTATGACCGTGGCCG 1 cca ( 1) CCCAAGCCGCAAACGCAAAGATCGCTGGATGAACTAAATCGCCTTCTTCG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCCAMGCAABVAMCBYAAAAHCACCABCATVMACTAAATCASYDWGTTSG MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 50 n= 13770 bayes= 12.486 E= 1.2e-001 -865 12 180 -865 -13 170 -865 -865 -865 212 -865 -865 146 -865 -865 -17 87 112 -865 -865 -865 -865 221 -865 -865 212 -865 -865 146 12 -865 -865 146 -865 22 -865 -865 12 122 -17 -13 112 22 -865 146 12 -865 -865 87 112 -865 -865 -865 212 -865 -865 -865 12 22 83 -865 112 -865 83 187 -865 -865 -865 187 -865 -865 -865 187 -865 -865 -865 146 -865 22 -865 -13 12 -865 83 -865 170 -865 -17 146 12 -865 -865 -865 170 22 -865 -865 170 22 -865 146 -865 -865 -17 -865 12 22 83 -865 170 22 -865 187 -865 -865 -865 -865 12 -865 141 87 12 22 -865 87 112 -865 -865 187 -865 -865 -865 -865 170 22 -865 -865 -865 -865 182 146 12 -865 -865 146 -865 -865 -17 187 -865 -865 -865 -865 -865 -865 182 -865 170 22 -865 146 -865 22 -865 -865 112 122 -865 -865 112 -865 83 87 -865 22 -17 87 -865 -865 83 -865 12 180 -865 -865 -865 22 141 -865 12 -865 141 -865 112 122 -865 -865 -865 221 -865 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCCAMGCAABVAMCBYAAAAHCACCABCATVMACTAAATCASYDWGTTSG MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 50 nsites= 4 E= 1.2e-001 0.000000 0.250000 0.750000 0.000000 0.250000 0.750000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.750000 0.000000 0.000000 0.250000 0.500000 0.500000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.750000 0.250000 0.000000 0.000000 0.750000 0.000000 0.250000 0.000000 0.000000 0.250000 0.500000 0.250000 0.250000 0.500000 0.250000 0.000000 0.750000 0.250000 0.000000 0.000000 0.500000 0.500000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.250000 0.250000 0.500000 0.000000 0.500000 0.000000 0.500000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.750000 0.000000 0.250000 0.000000 0.250000 0.250000 0.000000 0.500000 0.000000 0.750000 0.000000 0.250000 0.750000 0.250000 0.000000 0.000000 0.000000 0.750000 0.250000 0.000000 0.000000 0.750000 0.250000 0.000000 0.750000 0.000000 0.000000 0.250000 0.000000 0.250000 0.250000 0.500000 0.000000 0.750000 0.250000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.250000 0.000000 0.750000 0.500000 0.250000 0.250000 0.000000 0.500000 0.500000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.750000 0.250000 0.000000 0.000000 0.000000 0.000000 1.000000 0.750000 0.250000 0.000000 0.000000 0.750000 0.000000 0.000000 0.250000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.750000 0.250000 0.000000 0.750000 0.000000 0.250000 0.000000 0.000000 0.500000 0.500000 0.000000 0.000000 0.500000 0.000000 0.500000 0.500000 0.000000 0.250000 0.250000 0.500000 0.000000 0.000000 0.500000 0.000000 0.250000 0.750000 0.000000 0.000000 0.000000 0.250000 0.750000 0.000000 0.250000 0.000000 0.750000 0.000000 0.500000 0.500000 0.000000 0.000000 0.000000 1.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCCAMGCAABVAMCBYAAAAHCACCABCATVMACTAAATCASYDWGTTSG MEME-1 regular expression -------------------------------------------------------------------------------- [GC][CA]C[AT][AC]GC[AC][AG][GCT][CAG][AC][AC]C[TCG][CT]AAA[AG][TAC][CT][AC][CG][CG][AT][TCG][CG]A[TC][ACG][AC]A[CG]T[AC][AT]AT[CG][AG][CG][CT][AGT][AT][GC][TG][TC][CG]G -------------------------------------------------------------------------------- Time 33.51 secs. ******************************************************************************** ******************************************************************************** MOTIF CCRBVCAGYHGCKGGAAGVGATSRASGMAKYBTTASA MEME-2 width = 37 sites = 8 llr = 187 E-value = 2.7e+000 ******************************************************************************** -------------------------------------------------------------------------------- Motif CCRBVCAGYHGCKGGAAGVGATSRASGMAKYBTTASA MEME-2 Description -------------------------------------------------------------------------------- Simplified A :13131611333::1a6:3:6::581:36111316:9 pos.-specific C 9814481:43:8::::::53::51:5:51143::36: probability G :15341:8:16:589:3a383144:4a1:313:::41 matrix T 1:13::31541:53::1:::191:3::13544891:: bits 2.2 * * 2.0 * * 1.8 * * * 1.6 * ** * * Relative 1.3 * * *** * * * * * * Entropy 1.1 ** * * ***** * * * * * ** ** (33.8 bits) 0.9 ** * * ****** * * * * * ** ** 0.7 ** *** ***************** * ***** 0.4 ** ***** ***************** * ***** 0.2 ********* ********************* ***** 0.0 ------------------------------------- Multilevel CCGCCCAGTTGCGGGAAGCGATCAACGCATCTTTACA consensus AGG T CAAATT G ACG GGTG ATGTCA CG sequence TA C G G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCRBVCAGYHGCKGGAAGVGATSRASGMAKYBTTASA MEME-2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------------------------------- rbsR 39 1.16e-14 GCACAACCTT CCGTACCGTGGCGTGAAGAGATCGACGCATTTTTAGA CAGGCAGAGG yciH 55 3.14e-13 TCGGTAGATC CAGCGCAGACACTGAAAGCGATCAACGCCTCTTTACA GCGGAGTGC yfeD 14 3.21e-12 CAGTTTACAT CCTTGCTTCTGCGGGAAGGGATTATCGGATTGTTACA ACGCTTAGGG fis 26 9.33e-12 ATTGAGGATG CCAGCGAACAGCTGGAGGCGTTGGAGGCATACTTCGA AAATTTTGCG yjjM 52 2.91e-11 TACTATACCG CGCCCCAGTATAGGGAAGGGGTGAAGGTAGCGTTTCA CGCGACCGCC holB 28 2.91e-11 ACCATTGATG CCACCCAGCCGCTGGAGGCCGTGATGGATGCAATCCG CACTACCGTG yqgE 18 5.30e-11 GTGTCGATCA CCGGAATGTTAATGGATGCCATCGAAGCACGTTTACA GCAGCAGTAA dnaN 23 3.17e-10 TGCCGTAAGA TCGAGCAGTTGCGTGAAGAGAGCCACGATATCAAAGA AGATTTTTCA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCRBVCAGYHGCKGGAAGVGATSRASGMAKYBTTASA MEME-2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- rbsR 1.2e-14 38_[+2]_25 yciH 3.1e-13 54_[+2]_9 yfeD 3.2e-12 13_[+2]_50 fis 9.3e-12 25_[+2]_38 yjjM 2.9e-11 51_[+2]_12 holB 2.9e-11 27_[+2]_36 yqgE 5.3e-11 17_[+2]_46 dnaN 3.2e-10 22_[+2]_41 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCRBVCAGYHGCKGGAAGVGATSRASGMAKYBTTASA MEME-2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF CCRBVCAGYHGCKGGAAGVGATSRASGMAKYBTTASA width=37 seqs=8 rbsR ( 39) CCGTACCGTGGCGTGAAGAGATCGACGCATTTTTAGA 1 yciH ( 55) CAGCGCAGACACTGAAAGCGATCAACGCCTCTTTACA 1 yfeD ( 14) CCTTGCTTCTGCGGGAAGGGATTATCGGATTGTTACA 1 fis ( 26) CCAGCGAACAGCTGGAGGCGTTGGAGGCATACTTCGA 1 yjjM ( 52) CGCCCCAGTATAGGGAAGGGGTGAAGGTAGCGTTTCA 1 holB ( 28) CCACCCAGCCGCTGGAGGCCGTGATGGATGCAATCCG 1 yqgE ( 18) CCGGAATGTTAATGGATGCCATCGAAGCACGTTTACA 1 dnaN ( 23) TCGAGCAGTTGCGTGAAGAGAGCCACGATATCAAAGA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCRBVCAGYHGCKGGAAGVGATSRASGMAKYBTTASA MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 37 n= 17280 bayes= 11.0761 E= 2.7e+000 -965 193 -965 -117 -113 170 -78 -965 -13 -88 122 -117 -113 70 22 -17 -13 70 80 -965 -113 170 -78 -965 119 -88 -965 -17 -113 -965 180 -117 -113 70 -965 83 -13 12 -78 41 -13 -965 154 -117 -13 170 -965 -965 -965 -965 122 83 -965 -965 180 -17 -113 -965 202 -965 187 -965 -965 -965 119 -965 22 -117 -965 -965 222 -965 -13 112 22 -965 -965 12 180 -965 119 -965 22 -117 -965 -965 -78 163 -965 112 80 -117 87 -88 80 -965 146 -965 -965 -17 -113 112 80 -965 -965 -965 222 -965 -13 112 -78 -117 119 -88 -965 -17 -113 -88 22 83 -113 70 -78 41 -113 12 22 41 -13 -965 -965 141 -113 -965 -965 163 119 12 -965 -117 -965 144 80 -965 168 -965 -78 -965 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCRBVCAGYHGCKGGAAGVGATSRASGMAKYBTTASA MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 37 nsites= 8 E= 2.7e+000 0.000000 0.875000 0.000000 0.125000 0.125000 0.750000 0.125000 0.000000 0.250000 0.125000 0.500000 0.125000 0.125000 0.375000 0.250000 0.250000 0.250000 0.375000 0.375000 0.000000 0.125000 0.750000 0.125000 0.000000 0.625000 0.125000 0.000000 0.250000 0.125000 0.000000 0.750000 0.125000 0.125000 0.375000 0.000000 0.500000 0.250000 0.250000 0.125000 0.375000 0.250000 0.000000 0.625000 0.125000 0.250000 0.750000 0.000000 0.000000 0.000000 0.000000 0.500000 0.500000 0.000000 0.000000 0.750000 0.250000 0.125000 0.000000 0.875000 0.000000 1.000000 0.000000 0.000000 0.000000 0.625000 0.000000 0.250000 0.125000 0.000000 0.000000 1.000000 0.000000 0.250000 0.500000 0.250000 0.000000 0.000000 0.250000 0.750000 0.000000 0.625000 0.000000 0.250000 0.125000 0.000000 0.000000 0.125000 0.875000 0.000000 0.500000 0.375000 0.125000 0.500000 0.125000 0.375000 0.000000 0.750000 0.000000 0.000000 0.250000 0.125000 0.500000 0.375000 0.000000 0.000000 0.000000 1.000000 0.000000 0.250000 0.500000 0.125000 0.125000 0.625000 0.125000 0.000000 0.250000 0.125000 0.125000 0.250000 0.500000 0.125000 0.375000 0.125000 0.375000 0.125000 0.250000 0.250000 0.375000 0.250000 0.000000 0.000000 0.750000 0.125000 0.000000 0.000000 0.875000 0.625000 0.250000 0.000000 0.125000 0.000000 0.625000 0.375000 0.000000 0.875000 0.000000 0.125000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCRBVCAGYHGCKGGAAGVGATSRASGMAKYBTTASA MEME-2 regular expression -------------------------------------------------------------------------------- CC[GA][CGT][CGA]C[AT]G[TC][TAC][GA][CA][GT][GT]GA[AG]G[CAG][GC][AG]T[CG][AG][AT][CG]G[CA][AT][TG][CT][TCG][TA]T[AC][CG]A -------------------------------------------------------------------------------- Time 65.65 secs. ******************************************************************************** ******************************************************************************** MOTIF GDCCTWCWCCGACGGGCACWTC MEME-3 width = 22 sites = 4 llr = 94 E-value = 8.6e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif GDCCTWCWCCGACGGGCACWTC MEME-3 Description -------------------------------------------------------------------------------- Simplified A :5:::5:53:38:::::a:5:: pos.-specific C ::aa::8:88:3a::3a:a::a probability G a3::3:3::38::8a8:::::: matrix T :3::85:5:::::3:::::5a: bits 2.2 * ** * * * * * 2.0 * ** * * * * * 1.8 * ** * * *** ** 1.6 * ** * * *** ** Relative 1.3 * ** * *** ******* ** Entropy 1.1 * *** * *********** ** (34.0 bits) 0.9 * ******************** 0.7 * ******************** 0.4 ********************** 0.2 ********************** 0.0 ---------------------- Multilevel GACCTACACCGACGGGCACATC consensus G GTGTAGAC T C T sequence T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GDCCTWCWCCGACGGGCACWTC MEME-3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------------- gntR 68 6.68e-12 TGGGCATGAA GTCCTACACCGACTGGCACATC CGCACTGGTT rplC 24 6.68e-12 AGACTACGCA GACCTAGACCGACGGCCACATC TGCACGTCTA rpsE 48 9.58e-12 ACAGGTCCGT GACCGTCTACGACGGGCACTTC GACCGGAAGT rpmC 15 4.70e-11 CCCGCCACAA GGCCTTCTCGACCGGGCACTTC GTAAGTTCGA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GDCCTWCWCCGACGGGCACWTC MEME-3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- gntR 6.7e-12 67_[+3]_11 rplC 6.7e-12 23_[+3]_55 rpsE 9.6e-12 47_[+3]_31 rpmC 4.7e-11 14_[+3]_64 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GDCCTWCWCCGACGGGCACWTC MEME-3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF GDCCTWCWCCGACGGGCACWTC width=22 seqs=4 gntR ( 68) GTCCTACACCGACTGGCACATC 1 rplC ( 24) GACCTAGACCGACGGCCACATC 1 rpsE ( 48) GACCGTCTACGACGGGCACTTC 1 rpmC ( 15) GGCCTTCTCGACCGGGCACTTC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GDCCTWCWCCGACGGGCACWTC MEME-3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 22 n= 21330 bayes= 13.1174 E= 8.6e+001 -865 -865 221 -865 87 -865 22 -17 -865 212 -865 -865 -865 212 -865 -865 -865 -865 22 141 87 -865 -865 83 -865 170 22 -865 87 -865 -865 83 -13 170 -865 -865 -865 170 22 -865 -13 -865 180 -865 146 12 -865 -865 -865 212 -865 -865 -865 -865 180 -17 -865 -865 221 -865 -865 12 180 -865 -865 212 -865 -865 187 -865 -865 -865 -865 212 -865 -865 87 -865 -865 83 -865 -865 -865 182 -865 212 -865 -865 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GDCCTWCWCCGACGGGCACWTC MEME-3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 22 nsites= 4 E= 8.6e+001 0.000000 0.000000 1.000000 0.000000 0.500000 0.000000 0.250000 0.250000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.250000 0.750000 0.500000 0.000000 0.000000 0.500000 0.000000 0.750000 0.250000 0.000000 0.500000 0.000000 0.000000 0.500000 0.250000 0.750000 0.000000 0.000000 0.000000 0.750000 0.250000 0.000000 0.250000 0.000000 0.750000 0.000000 0.750000 0.250000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.750000 0.250000 0.000000 0.000000 1.000000 0.000000 0.000000 0.250000 0.750000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.500000 0.000000 0.000000 0.500000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GDCCTWCWCCGACGGGCACWTC MEME-3 regular expression -------------------------------------------------------------------------------- G[AGT]CC[TG][AT][CG][AT][CA][CG][GA][AC]C[GT]G[GC]CAC[AT]TC -------------------------------------------------------------------------------- Time 97.19 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- nhaR 3.93e-01 100 rpsT 2.94e-01 100 polB 9.92e-01 100 leuO 9.83e-01 100 fruR 9.69e-01 100 pdhR 6.22e-01 100 pcnB 4.23e-01 100 rpsB 1.91e-01 100 tsf 6.79e-02 100 dnaE 6.71e-02 100 yaeO 9.38e-02 100 yafC 7.69e-01 100 dnaQ 1.10e-01 100 dinP 8.82e-01 100 yajF 6.33e-01 100 nrdR 6.78e-01 100 nusB 5.36e-02 100 ybaO 9.85e-02 100 acrR 7.74e-01 100 dnaX 9.14e-01 100 ybbI 5.09e-01 100 ybbS 2.19e-01 100 ybbU 5.09e-01 100 entF 2.76e-01 100 cds-NP_706461.1 9.37e-01 100 rnk 2.07e-02 20_[+3(9.89e-05)]_58 farR 5.43e-01 100 nagC 9.03e-03 100 holA 1.49e-01 100 ybiH 6.77e-01 100 cds-NP_706694.1 6.52e-01 100 deoR 2.21e-01 100 rimK 4.85e-03 100 infA 2.12e-02 100 lrp 3.92e-01 100 cds-NP_706797.1 1.44e-01 100 cds-NP_706801.1 3.26e-01 100 rpsA 5.68e-02 100 cds-NP_706932.1 8.18e-01 100 ycdC 4.81e-01 100 rimJ 2.41e-01 100 rpmF 5.28e-01 100 holB 3.60e-09 27_[+2(2.91e-11)]_36 ycfQ 9.98e-01 100 mfd 6.53e-01 100 ycfX 1.67e-01 100 umuD 8.67e-01 100 umuC 1.84e-02 100 fadR 9.33e-01 100 cds-NP_707110.1 6.34e-01 100 ychF 1.20e-01 100 yciO 5.55e-01 100 cysB 9.55e-01 100 yciH 3.56e-09 54_[+2(3.14e-13)]_9 cds-NP_707193.1 6.98e-01 100 ycjC 8.18e-02 100 pspF 5.62e-01 100 pspC 2.06e-01 100 ycjW 3.64e-01 100 tyrR 9.10e-01 100 cds-NP_707242.1 9.50e-02 100 cds-NP_707292.1 9.42e-01 100 cds-NP_707313.1 5.52e-01 100 cds-NP_707343.1 9.71e-01 100 infC 8.07e-02 100 rpmI 9.11e-01 100 rplT 6.03e-01 100 relE 1.88e-02 17_[+3(8.51e-05)]_61 marR 2.96e-01 100 ydeW 5.98e-01 100 mlc 6.43e-01 100 ynfL 3.36e-01 100 uidR 2.99e-01 100 malI 3.62e-01 100 slyA 6.77e-01 100 cds-NP_707550.2 1.53e-01 100 rnt 5.74e-01 100 ydhB 7.14e-01 100 cds-NP_707629.1 8.92e-01 100 cds-NP_707644.1 6.17e-01 100 rimL 7.97e-01 100 cds-NP_707650.1 5.64e-01 100 cds-NP_707706.2 8.11e-03 76_[+3(8.28e-05)]_2 yebK 2.87e-01 100 cds-NP_707754.1 5.86e-01 100 cbl 4.01e-01 100 nac 7.70e-01 100 yeeY 4.07e-01 100 gatR 8.10e-02 100 galS 4.72e-01 100 yeiE 9.94e-01 100 yeiP 3.35e-01 100 rplY 7.76e-01 100 lrhA 2.85e-01 100 cds-NP_708235.2 6.79e-01 100 yfeD 6.33e-09 13_[+2(3.21e-12)]_50 yfeR 5.44e-01 100 yfeT 9.18e-02 100 cds-NP_708290.1 2.67e-01 100 cds-NP_708370.1 8.33e-02 100 csiE 9.20e-01 100 hcaR 3.61e-01 100 yphH 6.89e-01 100 yfhH 6.96e-01 100 rpoE 4.62e-01 100 yfiE 5.22e-01 100 rplS 8.20e-01 100 rpsP 9.85e-01 100 ygaE 9.42e-01 100 cds-NP_708481.1 9.76e-01 100 srlR 9.37e-01 100 ygaA 9.21e-01 100 ascG 2.61e-01 100 fhlA 6.15e-01 100 ygbI 7.70e-01 100 cds-NP_708541.1 6.61e-01 100 cds-NP_708545.1 1.08e-01 100 cds-NP_708546.1 1.17e-01 100 fucR 3.14e-01 100 gcvA 9.98e-01 100 galR 3.88e-01 100 lysR 8.14e-01 100 iciA 7.31e-01 100 ygfI 1.93e-01 100 yggD 8.02e-01 100 gshB 4.99e-01 100 yqgE 8.22e-08 17_[+2(5.30e-11)]_46 cds-NP_708761.1 4.15e-01 100 glcC 9.34e-01 100 cds-NP_708799.2 7.43e-01 100 cca 2.52e-14 [+1(2.89e-18)]_50 ygiP 9.47e-01 100 rpsU 3.47e-01 100 rpoD 2.87e-01 100 yqjI 7.09e-01 100 ebgR 2.52e-01 100 ygjM 5.38e-01 100 exuR 1.62e-01 100 yhaJ 2.59e-01 100 yhaR 3.99e-01 100 tdcA 4.38e-01 100 agaR 2.96e-01 100 rpsO 2.34e-01 100 infB 3.15e-02 100 nusA 2.22e-01 100 greA 2.71e-01 100 rpmA 9.48e-02 100 rplU 3.11e-02 100 nlp 6.36e-01 100 yrbA 4.80e-02 100 rpoN 8.88e-01 100 yhcI 4.85e-02 100 yhcK 1.04e-01 100 rpsI 2.82e-01 100 rplM 5.08e-01 100 yhcS 3.77e-01 100 prmA 3.83e-01 100 fis 1.70e-09 25_[+2(9.33e-12)]_38 yrdC 8.70e-01 100 rplQ 9.84e-01 100 rpoA 3.56e-01 100 rpsD 8.20e-01 100 rpsK 7.57e-01 100 rpsM 9.85e-01 100 rpmJ 1.77e-01 100 rplO 5.53e-01 100 rpmD 7.98e-01 100 rpsE 9.68e-08 47_[+3(9.58e-12)]_31 rplR 8.52e-01 100 rplF 5.11e-03 100 rpsH 7.39e-01 100 rpsN 2.51e-01 100 rplE 5.97e-01 100 rplX 3.79e-01 100 rplN 1.90e-01 100 rpsQ 3.61e-01 100 rpmC 1.63e-08 14_[+3(4.70e-11)]_64 rplP 5.51e-02 100 rpsC 5.63e-01 100 rplV 8.31e-01 100 rpsS 4.85e-01 100 rplB 2.00e-01 100 rplW 4.89e-01 100 rplD 1.31e-01 100 rplC 1.34e-08 23_[+3(6.68e-12)]_55 rpsJ 8.03e-01 100 tuf 6.56e-01 100 fusA 2.10e-01 100 rpsG 9.57e-01 100 rpsL 6.91e-01 100 yhfR 5.55e-01 100 greB 9.31e-01 100 yhgF 3.32e-03 100 rtcR 5.93e-01 100 glpR 5.29e-02 21_[+1(9.75e-05)]_29 gntR 4.68e-08 67_[+3(6.68e-12)]_11 rpoH 7.84e-02 100 yhhG 1.88e-01 100 cds-NP_709283.2 4.42e-25 25_[+1(1.44e-28)]_25 yhjC 3.72e-01 100 yiaJ 9.44e-01 100 selB 1.22e-01 100 mtlR 5.10e-01 100 lldR 3.71e-02 100 rpmG 3.70e-02 47_[+3(3.39e-05)]_31 rpmB 6.99e-01 100 ttk 7.06e-01 100 rpoZ 9.29e-01 100 bglG 4.56e-01 100 dnaN 4.30e-07 22_[+2(3.17e-10)]_41 yidW 5.00e-01 100 yidP 6.77e-01 100 atpC 4.94e-01 100 atpD 6.40e-01 100 atpG 7.13e-01 100 atpA 3.29e-01 100 atpH 7.07e-02 100 atpF 4.08e-01 100 atpE 7.30e-01 100 atpB 6.14e-15 20_[+1(2.22e-18)]_30 atpI 2.15e-01 100 asnC_2 8.55e-01 100 rbsR 1.68e-10 38_[+2(1.16e-14)]_25 yieP 8.92e-01 100 yifA 8.54e-01 100 ilvY 5.03e-01 100 rho 3.89e-01 100 metR 1.38e-01 100 rfaH 2.59e-01 100 polA 7.83e-01 100 yihL 9.59e-01 100 yihW 9.59e-01 100 cytR 2.18e-01 100 rpmE 4.89e-01 100 metJ 4.85e-01 100 oxyR 7.97e-01 100 yijC 4.23e-01 100 tuf_2 7.08e-01 100 nusG 7.02e-01 100 rplK 3.53e-01 100 rplA 8.39e-01 100 rplJ 4.66e-01 100 rplL 7.60e-01 100 rpoB 2.88e-01 100 rpoC 6.74e-02 100 iclR 6.97e-01 100 sorC 4.41e-01 100 soxR 8.11e-01 100 lexA 2.51e-01 100 yjiE 4.00e-01 100 uxuR 5.05e-02 100 cds-NP_709929.2 2.21e-24 1_[+1(1.44e-28)]_49 holC 5.74e-01 100 yjgJ 7.72e-01 100 yjgH 3.81e-01 100 yjgF 8.09e-01 100 treR 4.19e-01 100 ytfJ 5.37e-01 100 ytfH 8.61e-01 100 ytfA 6.07e-01 100 efp 9.73e-01 100 yjeB 1.60e-01 100 yjfQ 6.11e-01 100 rpsF 2.28e-01 100 rpsR 4.37e-01 100 rplI 7.44e-01 100 hpcR 3.45e-01 100 yjjM 1.61e-07 51_[+2(2.91e-11)]_12 holD 2.97e-01 100 cds-NP_710125.1 3.07e-02 100 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (3) found. ******************************************************************************** CPU: kodomo ********************************************************************************