******************************************************************************** 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= proms_100.fasta CONTROL SEQUENCES= --none-- ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ "gadA" 1.0000 50 "yhiR" 1.0000 50 "CP0090" 1.0000 50 "SF2066" 1.0000 50 "yraM" 1.0000 50 "ibpA" 1.0000 50 "yhgA" 1.0000 50 "ygiM" 1.0000 50 "hdeD" 1.0000 50 "rpsB" 1.0000 50 "SF1596" 1.0000 50 "SF0837" 1.0000 50 "helD" 1.0000 50 "SF1484" 1.0000 50 "yejL" 1.0000 50 "yjfM" 1.0000 50 "yehL" 1.0000 50 "ygiX" 1.0000 50 "ychP" 1.0000 50 "SF1497" 1.0000 50 "efp" 1.0000 50 "SF3641" 1.0000 50 "shiB" 1.0000 50 "SF3992" 1.0000 50 "fucP" 1.0000 50 "yhjC" 1.0000 50 "tap" 1.0000 50 "SF2046" 1.0000 50 "yhhA" 1.0000 50 "feoA" 1.0000 50 "SF1897" 1.0000 50 "SF2332" 1.0000 50 "ynfM" 1.0000 50 "ybiK" 1.0000 50 "SF1037" 1.0000 50 "SF1089" 1.0000 50 "SF1670" 1.0000 50 "hpt" 1.0000 50 "yfeK" 1.0000 50 "iciA" 1.0000 50 "ycbS" 1.0000 50 "secE" 1.0000 50 "yhcN" 1.0000 50 "queA" 1.0000 50 "ybjM" 1.0000 50 "SF3082" 1.0000 50 "SF2017" 1.0000 50 "dcp" 1.0000 50 "pitA" 1.0000 50 "yeiQ" 1.0000 50 "SF0494" 1.0000 50 "yheS" 1.0000 50 "SF2051" 1.0000 50 "CP0184" 1.0000 50 "CP0163" 1.0000 50 "purM" 1.0000 50 "rplJ" 1.0000 50 "creA" 1.0000 50 "osmY" 1.0000 50 "SF0591" 1.0000 50 "csgB" 1.0000 50 "SF1788" 1.0000 50 "ppsA" 1.0000 50 "ybiN" 1.0000 50 "pgpB" 1.0000 50 "yajQ" 1.0000 50 "yadG" 1.0000 50 "CP0233" 1.0000 50 "yiiS" 1.0000 50 "trxA" 1.0000 50 "yacK" 1.0000 50 "ccrB" 1.0000 50 "yjeB" 1.0000 50 "yfiK" 1.0000 50 "argR" 1.0000 50 "phoB" 1.0000 50 "yajF" 1.0000 50 "SF3003" 1.0000 50 "SF2045" 1.0000 50 "lpp" 1.0000 50 "torC" 1.0000 50 "yfaO" 1.0000 50 "ybgD" 1.0000 50 "SF1025" 1.0000 50 "ppa" 1.0000 50 "SF1927" 1.0000 50 "yedA" 1.0000 50 "entF" 1.0000 50 "ychE" 1.0000 50 "ubiG" 1.0000 50 "polA" 1.0000 50 "sfmA" 1.0000 50 "mutH" 1.0000 50 "SF3639" 1.0000 50 "SF2406" 1.0000 50 "iap" 1.0000 50 "yhfC" 1.0000 50 "SF2551" 1.0000 50 "SF0519" 1.0000 50 "ushA" 1.0000 50 ******************************************************************************** ******************************************************************************** COMMAND LINE SUMMARY ******************************************************************************** This information can also be useful in the event you wish to report a problem with the MEME software. command: meme proms_100.fasta -dna -nmotifs 1 -minw 5 -maxw 8 model: mod= zoops nmotifs= 1 evt= inf objective function: em= E-value of product of p-values starts= E-value of product of p-values strands: + width: minw= 5 maxw= 8 nsites: minsites= 2 maxsites= 100 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= 5000 N= 100 sample: seed= 0 hsfrac= 0 searchsize= 5000 norand= no csites= 1000 Letter frequencies in dataset: A 0.304 C 0.198 G 0.211 T 0.287 Background letter frequencies (from file dataset with add-one prior applied): A 0.304 C 0.198 G 0.211 T 0.287 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF GCKCCCCG MEME-1 width = 8 sites = 5 llr = 57 E-value = 8.4e+000 ******************************************************************************** -------------------------------------------------------------------------------- Motif GCKCCCCG MEME-1 Description -------------------------------------------------------------------------------- Simplified A :::::::: pos.-specific C :a:aa8a: probability G a:6::2:a matrix T ::4::::: bits 2.3 ** ** ** 2.1 ** ** ** 1.9 ** ** ** 1.6 ** ***** Relative 1.4 ** ***** Entropy 1.2 ******** (16.5 bits) 0.9 ******** 0.7 ******** 0.5 ******** 0.2 ******** 0.0 -------- Multilevel GCGCCCCG consensus T G sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCKCCCCG MEME-1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- "queA" 1 2.86e-06 . GCGCCCCG GCACTAGACT "yhiR" 4 2.86e-06 TGT GCGCCCCG AATACGGGCC "SF0591" 17 6.75e-06 ACGAAAGCGC GCTCCCCG CAAGCAACTA "SF1897" 7 6.75e-06 GTACCT GCTCCCCG TGGTTATCTG "pitA" 14 9.79e-06 CACTGATAAT GCGCCGCG TTCATGTCCT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCKCCCCG MEME-1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- "queA" 2.9e-06 [+1]_42 "yhiR" 2.9e-06 3_[+1]_39 "SF0591" 6.7e-06 16_[+1]_26 "SF1897" 6.7e-06 6_[+1]_36 "pitA" 9.8e-06 13_[+1]_29 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCKCCCCG MEME-1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF GCKCCCCG width=8 seqs=5 "queA" ( 1) GCGCCCCG 1 "yhiR" ( 4) GCGCCCCG 1 "SF0591" ( 17) GCTCCCCG 1 "SF1897" ( 7) GCTCCCCG 1 "pitA" ( 14) GCGCCGCG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCKCCCCG MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 4300 bayes= 10.6907 E= 8.4e+000 -897 -897 224 -897 -897 233 -897 -897 -897 -897 151 48 -897 233 -897 -897 -897 233 -897 -897 -897 201 -8 -897 -897 233 -897 -897 -897 -897 224 -897 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCKCCCCG MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 5 E= 8.4e+000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.600000 0.400000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.800000 0.200000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCKCCCCG MEME-1 regular expression -------------------------------------------------------------------------------- GC[GT]CC[CG]CG -------------------------------------------------------------------------------- Time 1.12 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- "gadA" 9.99e-01 50 "yhiR" 1.23e-04 3_[+1(2.86e-06)]_39 "CP0090" 4.06e-01 50 "SF2066" 1.75e-01 50 "yraM" 6.02e-01 50 "ibpA" 5.52e-01 50 "yhgA" 1.40e-01 50 "ygiM" 4.45e-01 50 "hdeD" 9.86e-01 50 "rpsB" 7.31e-01 50 "SF1596" 1.60e-01 50 "SF0837" 1.00e+00 50 "helD" 9.65e-01 50 "SF1484" 1.40e-01 50 "yejL" 5.52e-01 50 "yjfM" 5.74e-01 50 "yehL" 5.52e-01 50 "ygiX" 6.51e-01 50 "ychP" 5.52e-01 50 "SF1497" 9.40e-01 50 "efp" 2.82e-01 50 "SF3641" 7.34e-01 50 "shiB" 8.96e-01 50 "SF3992" 6.02e-01 50 "fucP" 9.65e-01 50 "yhjC" 2.46e-01 50 "tap" 2.65e-02 50 "SF2046" 9.15e-02 50 "yhhA" 1.75e-01 50 "feoA" 3.39e-02 50 "SF1897" 2.90e-04 6_[+1(6.75e-06)]_36 "SF2332" 5.97e-02 50 "ynfM" 4.45e-01 50 "ybiK" 2.23e-01 50 "SF1037" 5.52e-01 50 "SF1089" 1.75e-01 50 "SF1670" 1.00e+00 50 "hpt" 9.15e-02 50 "yfeK" 9.70e-01 50 "iciA" 9.84e-01 50 "ycbS" 7.62e-01 50 "secE" 5.74e-01 50 "yhcN" 1.00e+00 50 "queA" 1.23e-04 [+1(2.86e-06)]_42 "ybjM" 6.51e-01 50 "SF3082" 4.45e-01 50 "SF2017" 5.52e-01 50 "dcp" 1.80e-01 50 "pitA" 4.21e-04 13_[+1(9.79e-06)]_29 "yeiQ" 8.96e-01 50 "SF0494" 4.45e-01 50 "yheS" 6.14e-01 50 "SF2051" 5.52e-01 50 "CP0184" 4.72e-01 50 "CP0163" 7.62e-01 50 "purM" 1.29e-01 50 "rplJ" 8.37e-01 50 "creA" 8.96e-01 50 "osmY" 7.17e-01 50 "SF0591" 2.90e-04 16_[+1(6.75e-06)]_26 "csgB" 3.86e-01 50 "SF1788" 5.74e-01 50 "ppsA" 8.37e-01 50 "ybiN" 8.96e-01 50 "pgpB" 9.94e-01 50 "yajQ" 1.60e-01 50 "yadG" 9.98e-01 50 "CP0233" 7.17e-01 50 "yiiS" 5.52e-01 50 "trxA" 4.72e-01 50 "yacK" 7.07e-02 50 "ccrB" 7.17e-01 50 "yjeB" 5.52e-01 50 "yfiK" 1.75e-01 50 "argR" 9.98e-01 50 "phoB" 6.14e-01 50 "yajF" 1.29e-01 50 "SF3003" 7.17e-01 50 "SF2045" 5.52e-01 50 "lpp" 4.72e-01 50 "torC" 4.45e-01 50 "yfaO" 9.65e-01 50 "ybgD" 3.86e-01 50 "SF1025" 3.08e-01 50 "ppa" 8.62e-01 50 "SF1927" 2.82e-01 50 "yedA" 1.29e-01 50 "entF" 2.23e-01 50 "ychE" 6.51e-01 50 "ubiG" 9.65e-01 50 "polA" 8.37e-01 50 "sfmA" 9.84e-01 50 "mutH" 8.62e-01 50 "SF3639" 9.86e-01 50 "SF2406" 1.75e-01 50 "iap" 9.99e-01 50 "yhfC" 1.06e-01 50 "SF2551" 1.00e+00 50 "SF0519" 7.17e-01 50 "ushA" 1.40e-01 50 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (1) found. ******************************************************************************** CPU: kodomo ********************************************************************************