******************************************************************************** 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= train.fa CONTROL SEQUENCES= --none-- ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ seq1_BACSU 1.0000 100 seq2_BACSU 1.0000 100 seq3_BACSU 1.0000 100 seq4_BACSU 1.0000 100 seq5_BACSU 1.0000 100 seq6_BACSU 1.0000 100 seq7_BACSU 1.0000 100 seq8_BACSU 1.0000 100 seq9_BACSU 1.0000 100 seq10_BACSU 1.0000 100 seq11_BACSU 1.0000 100 seq12_BACSU 1.0000 100 seq13_BACSU 1.0000 100 seq14_BACSU 1.0000 100 seq15_BACSU 1.0000 100 seq16_BACSU 1.0000 100 seq17_BACSU 1.0000 100 seq18_BACSU 1.0000 100 seq19_BACSU 1.0000 100 seq20_BACSU 1.0000 100 seq21_BACSU 1.0000 100 seq22_BACSU 1.0000 100 seq23_BACSU 1.0000 100 seq24_BACSU 1.0000 100 seq25_BACSU 1.0000 100 seq26_BACSU 1.0000 100 seq27_BACSU 1.0000 100 seq28_BACSU 1.0000 100 seq29_BACSU 1.0000 100 seq30_BACSU 1.0000 100 seq31_BACSU 1.0000 100 seq32_BACSU 1.0000 100 seq33_BACSU 1.0000 100 seq34_BACSU 1.0000 100 seq35_BACSU 1.0000 100 seq36_BACSU 1.0000 100 seq37_BACSU 1.0000 100 seq38_BACSU 1.0000 100 seq39_BACSU 1.0000 100 seq40_BACSU 1.0000 100 seq41_BACSU 1.0000 100 seq42_BACSU 1.0000 100 seq43_BACSU 1.0000 100 seq44_BACSU 1.0000 100 seq45_BACSU 1.0000 100 seq46_BACSU 1.0000 100 seq47_BACSU 1.0000 100 seq48_BACSU 1.0000 100 seq49_BACSU 1.0000 100 seq50_BACSU 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 train.fa -dna -minw 5 -maxw 50 -nmotifs 3 -text 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= 5 maxw= 50 nsites: minsites= 2 maxsites= 50 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= 50 sample: seed= 0 hsfrac= 0 searchsize= 5000 norand= no csites= 1000 Letter frequencies in dataset: A 0.327 C 0.157 G 0.222 T 0.294 Background letter frequencies (from file dataset with add-one prior applied): A 0.327 C 0.157 G 0.222 T 0.294 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF AAAGGAGR MEME-1 width = 8 sites = 50 llr = 295 E-value = 4.6e-012 ******************************************************************************** -------------------------------------------------------------------------------- Motif AAAGGAGR MEME-1 Description -------------------------------------------------------------------------------- Simplified A 668::6:3 pos.-specific C 1::::::1 probability G 132aa195 matrix T 21:::311 bits 2.7 2.4 2.1 ** 1.9 ** Relative 1.6 ** * Entropy 1.3 ** * (8.5 bits) 1.1 *** * 0.8 *** * 0.5 ****** 0.3 ******** 0.0 -------- Multilevel AAAGGAGG consensus TG T A sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAAGGAGR MEME-1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- seq50_BACSU 85 2.78e-05 TGTTTGTAAA AAAGGAGG AAAAATGA seq44_BACSU 79 2.78e-05 TTTTCTAAGA AAAGGAGG GACGTGCCGG seq28_BACSU 85 2.78e-05 TATAATAAAA AAAGGAGG GGCCTATT seq7_BACSU 83 2.78e-05 TCCGACTTAA AAAGGAGG ATGATTCAAA seq6_BACSU 83 2.78e-05 AAATAAAACC AAAGGAGG AGTCACATTA seq5_BACSU 85 2.78e-05 ATGTAGGCGA AAAGGAGG GAAAATAA seq30_BACSU 80 1.37e-04 TCTAAAACAG AAAGGAGA TTGGAGCGTG seq16_BACSU 84 1.37e-04 TAATACATGT AAAGGAGA GTATGTGAA seq47_BACSU 83 1.73e-04 TTTCGATTTA AAGGGAGG CTATGTGACT seq23_BACSU 85 1.73e-04 TTATGTGTAT AAGGGAGG AAATATGA seq10_BACSU 84 1.90e-04 TTGCCAAAAA TGAGGAGG ATCATAGAA seq49_BACSU 82 2.56e-04 CAACAGATCA CAAGGAGG ACGTTATCTT seq20_BACSU 23 2.56e-04 AAAAATTTAA CAAGGAGG ACGAGAGAAT seq34_BACSU 87 3.47e-04 CATTCTTATG AAAGGAGT TAAACA seq9_BACSU 85 3.47e-04 ATCAATAAAA AAAGGAGT GTTTCGCA seq40_BACSU 85 4.30e-04 CATATGGATG TAAGGAGA GAAATAGA seq15_BACSU 84 4.30e-04 CAATTTATTT TAAGGAGA CCGATTCTA seq41_BACSU 84 4.79e-04 GATGAATAAC GGAGGAGG GCAAACCCG seq33_BACSU 87 4.79e-04 AAACGGAAAA AAGGGTGG ATCTCA seq26_BACSU 10 4.79e-04 TTTTTCTAA AAGGGTGG TACCGCGAGA seq18_BACSU 81 4.79e-04 GTATATTCAA AAAGGAGC CCTTTATTGC seq46_BACSU 84 6.42e-04 AATGTGTAAA AAAGGGGG GCATGACCT seq43_BACSU 83 6.42e-04 GCTGACTGGT AAAGGGGG GCGTTCAAGA seq38_BACSU 37 6.42e-04 GGCAAAATGG ATAGGTGG TTGTCCATGT seq21_BACSU 86 6.42e-04 GCTTAAAACT AGAGGTGA TTATAGA seq32_BACSU 87 7.07e-04 TTTCAGGAAT TGAGGAGA ACAAAA seq24_BACSU 85 7.07e-04 AACCAACTTG TTAGGAGG CGTTTACA seq17_BACSU 85 7.07e-04 GACATTCTGA TTAGGAGG TTTCAAGA seq12_BACSU 83 7.07e-04 TTAATAATAC TTAGGAGG AAATTGATTA seq8_BACSU 85 7.07e-04 AACCATTATA TTAGGAGG AAATAACA seq27_BACSU 5 8.21e-04 ATCT AAAGGTGT GTTTGATAGA seq19_BACSU 87 9.92e-04 TTTAACGCAG TAAGGTGA TGAGTG seq4_BACSU 55 9.92e-04 CTGCAAGGAT CAGGGAGG TTATCTCGTC seq1_BACSU 89 9.92e-04 TATAGAAAGT AGGGGAGA AATA seq39_BACSU 87 1.03e-03 AGAAATATGT GGAGGTGG ATCATA seq22_BACSU 85 1.26e-03 TAGTAAAGGA AAAGGATG TGGCATCA seq35_BACSU 82 1.41e-03 GAAGAATAAG AAAGGCGG TTTCAAAGCA seq42_BACSU 87 1.55e-03 GCCCGTATCC ATAGGTGA CCTCCT seq29_BACSU 85 1.55e-03 ACACAAATAA AGAGGTGC TAAATTTT seq13_BACSU 83 1.55e-03 ACAGCAATTA GAAGGAGT TTGAATAATT seq25_BACSU 81 1.68e-03 TGCATACCAG TTAGGAGA ACAACGCGCA seq11_BACSU 87 1.78e-03 GCATGATTTG AGGGGTGA ATCAGT seq31_BACSU 90 2.18e-03 ATACTTTTGT GGAGGTGA CGA seq36_BACSU 88 2.35e-03 AATAATGTCT TAGGGTGA TATAA seq2_BACSU 84 2.35e-03 TTAGTTTTTG AAAGGGGT TTGTACGTT seq3_BACSU 88 2.79e-03 GTACAAAACA GGGGGAGA AGGCA seq48_BACSU 81 3.53e-03 TCCCATAATG AAAGGATT TGATTTTTGT seq37_BACSU 88 3.53e-03 TCCTTTTTTG CGAGGTGC TCCCA seq14_BACSU 85 4.46e-03 CGGTGAAGGC AGAGGTTA GATAAATA seq45_BACSU 16 5.87e-03 CCCAGTATAG TGAGGATT TTCGAGAATT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAAGGAGR MEME-1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- seq50_BACSU 2.8e-05 84_[+1]_8 seq44_BACSU 2.8e-05 78_[+1]_14 seq28_BACSU 2.8e-05 84_[+1]_8 seq7_BACSU 2.8e-05 82_[+1]_10 seq6_BACSU 2.8e-05 82_[+1]_10 seq5_BACSU 2.8e-05 84_[+1]_8 seq30_BACSU 0.00014 79_[+1]_13 seq16_BACSU 0.00014 83_[+1]_9 seq47_BACSU 0.00017 82_[+1]_10 seq23_BACSU 0.00017 84_[+1]_8 seq10_BACSU 0.00019 83_[+1]_9 seq49_BACSU 0.00026 81_[+1]_11 seq20_BACSU 0.00026 22_[+1]_70 seq34_BACSU 0.00035 86_[+1]_6 seq9_BACSU 0.00035 84_[+1]_8 seq40_BACSU 0.00043 84_[+1]_8 seq15_BACSU 0.00043 83_[+1]_9 seq41_BACSU 0.00048 83_[+1]_9 seq33_BACSU 0.00048 86_[+1]_6 seq26_BACSU 0.00048 9_[+1]_83 seq18_BACSU 0.00048 80_[+1]_12 seq46_BACSU 0.00064 83_[+1]_9 seq43_BACSU 0.00064 82_[+1]_10 seq38_BACSU 0.00064 36_[+1]_56 seq21_BACSU 0.00064 85_[+1]_7 seq32_BACSU 0.00071 86_[+1]_6 seq24_BACSU 0.00071 84_[+1]_8 seq17_BACSU 0.00071 84_[+1]_8 seq12_BACSU 0.00071 82_[+1]_10 seq8_BACSU 0.00071 84_[+1]_8 seq27_BACSU 0.00082 4_[+1]_88 seq19_BACSU 0.00099 86_[+1]_6 seq4_BACSU 0.00099 54_[+1]_38 seq1_BACSU 0.00099 88_[+1]_4 seq39_BACSU 0.001 86_[+1]_6 seq22_BACSU 0.0013 84_[+1]_8 seq35_BACSU 0.0014 81_[+1]_11 seq42_BACSU 0.0016 86_[+1]_6 seq29_BACSU 0.0016 84_[+1]_8 seq13_BACSU 0.0016 82_[+1]_10 seq25_BACSU 0.0017 80_[+1]_12 seq11_BACSU 0.0018 86_[+1]_6 seq31_BACSU 0.0022 89_[+1]_3 seq36_BACSU 0.0023 87_[+1]_5 seq2_BACSU 0.0023 83_[+1]_9 seq3_BACSU 0.0028 87_[+1]_5 seq48_BACSU 0.0035 80_[+1]_12 seq37_BACSU 0.0035 87_[+1]_5 seq14_BACSU 0.0045 84_[+1]_8 seq45_BACSU 0.0059 15_[+1]_77 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAAGGAGR MEME-1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF AAAGGAGR width=8 seqs=50 seq50_BACSU ( 85) AAAGGAGG 1 seq44_BACSU ( 79) AAAGGAGG 1 seq28_BACSU ( 85) AAAGGAGG 1 seq7_BACSU ( 83) AAAGGAGG 1 seq6_BACSU ( 83) AAAGGAGG 1 seq5_BACSU ( 85) AAAGGAGG 1 seq30_BACSU ( 80) AAAGGAGA 1 seq16_BACSU ( 84) AAAGGAGA 1 seq47_BACSU ( 83) AAGGGAGG 1 seq23_BACSU ( 85) AAGGGAGG 1 seq10_BACSU ( 84) TGAGGAGG 1 seq49_BACSU ( 82) CAAGGAGG 1 seq20_BACSU ( 23) CAAGGAGG 1 seq34_BACSU ( 87) AAAGGAGT 1 seq9_BACSU ( 85) AAAGGAGT 1 seq40_BACSU ( 85) TAAGGAGA 1 seq15_BACSU ( 84) TAAGGAGA 1 seq41_BACSU ( 84) GGAGGAGG 1 seq33_BACSU ( 87) AAGGGTGG 1 seq26_BACSU ( 10) AAGGGTGG 1 seq18_BACSU ( 81) AAAGGAGC 1 seq46_BACSU ( 84) AAAGGGGG 1 seq43_BACSU ( 83) AAAGGGGG 1 seq38_BACSU ( 37) ATAGGTGG 1 seq21_BACSU ( 86) AGAGGTGA 1 seq32_BACSU ( 87) TGAGGAGA 1 seq24_BACSU ( 85) TTAGGAGG 1 seq17_BACSU ( 85) TTAGGAGG 1 seq12_BACSU ( 83) TTAGGAGG 1 seq8_BACSU ( 85) TTAGGAGG 1 seq27_BACSU ( 5) AAAGGTGT 1 seq19_BACSU ( 87) TAAGGTGA 1 seq4_BACSU ( 55) CAGGGAGG 1 seq1_BACSU ( 89) AGGGGAGA 1 seq39_BACSU ( 87) GGAGGTGG 1 seq22_BACSU ( 85) AAAGGATG 1 seq35_BACSU ( 82) AAAGGCGG 1 seq42_BACSU ( 87) ATAGGTGA 1 seq29_BACSU ( 85) AGAGGTGC 1 seq13_BACSU ( 83) GAAGGAGT 1 seq25_BACSU ( 81) TTAGGAGA 1 seq11_BACSU ( 87) AGGGGTGA 1 seq31_BACSU ( 90) GGAGGTGA 1 seq36_BACSU ( 88) TAGGGTGA 1 seq2_BACSU ( 84) AAAGGGGT 1 seq3_BACSU ( 88) GGGGGAGA 1 seq48_BACSU ( 81) AAAGGATT 1 seq37_BACSU ( 88) CGAGGTGC 1 seq14_BACSU ( 85) AGAGGTTA 1 seq45_BACSU ( 16) TGAGGATT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAAGGAGR MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 4650 bayes= 6.52356 E= 4.6e-012 83 -97 -115 -29 87 -1229 23 -107 132 -1229 -30 -1229 -1229 -1229 217 -1229 -1229 -1229 217 -1229 97 -297 -189 -7 -1229 -1229 205 -188 -13 -138 117 -107 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAAGGAGR MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 50 E= 4.6e-012 0.580000 0.080000 0.100000 0.240000 0.600000 0.000000 0.260000 0.140000 0.820000 0.000000 0.180000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.640000 0.020000 0.060000 0.280000 0.000000 0.000000 0.920000 0.080000 0.300000 0.060000 0.500000 0.140000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAAGGAGR MEME-1 regular expression -------------------------------------------------------------------------------- [AT][AG]AGG[AT]G[GA] -------------------------------------------------------------------------------- Time 2.50 secs. ******************************************************************************** ******************************************************************************** MOTIF GKGCWKTTTTTWTTTTBKRWRA MEME-2 width = 22 sites = 19 llr = 217 E-value = 2.8e-006 ******************************************************************************** -------------------------------------------------------------------------------- Motif GKGCWKTTTTTWTTTTBKRWRA MEME-2 Description -------------------------------------------------------------------------------- Simplified A 1:2241::::142121::5559 pos.-specific C 111612:11:11211:42211: probability G 8652232::::21121453:31 matrix T :32:45899a83586823142: bits 2.7 2.4 2.1 1.9 * Relative 1.6 *** Entropy 1.3 * *** * (16.5 bits) 1.1 * * **** * * 0.8 ** * ***** * *** * 0.5 ** * ***** * *** * * 0.3 **** ****** ******** * 0.0 ---------------------- Multilevel GGGCATTTTTTATTTTCGAAAA consensus TTGTG TC A GTGTG sequence T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GKGCWKTTTTTWTTTTBKRWRA MEME-2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------------- seq9_BACSU 53 2.09e-11 ATGGGGATGA GGGCTCTTTTTATTTTCGATAA ATCAATAAAA seq26_BACSU 57 4.85e-11 TGGGATGAGA GGGCTTTTTTTATTTTCTGAAA AAATGCAGTG seq48_BACSU 35 8.56e-08 AAAGAAGCAT GGTCAGTTTTTAATTTGGGATA AAGGTTCAGC seq50_BACSU 62 2.82e-07 TTATTGGGAT GGGCTCTTTTTTGTGTTTGTAA AAAAGGAGGA seq10_BACSU 61 4.87e-07 GTTGATTGGT GTCCGTTTTTTATTTGCCAAAA ATGAGGAGGA seq21_BACSU 59 7.37e-07 GGCTTGAATA GGCCAAGTTTTTCTTTCGCTTA AAACTAGAGG seq41_BACSU 10 9.01e-07 TAATATTAG GTGAGTTTTTTGTTATGTAAAA AGAGCTTTTG seq6_BACSU 51 9.01e-07 CGAATAGAGC AGACGGTTTTTATTTTCCACAA AAATAAAACC seq30_BACSU 15 1.46e-06 GTGGTAAACA GGGGATTTTTACATATCGCAAA AATAATCAAA seq44_BACSU 32 1.76e-06 AGCGCCATTT GCTCTTTTTTTGTGTTCTATAA CAGAGAAAGA seq24_BACSU 36 5.39e-06 ATAACGGCAG GGGGATTTTTTATTTTTGTCCG CCTTGTTATG seq37_BACSU 23 5.83e-06 CGCTAAAGTT GTGGCCTTTTCGCTTTGTCATA TTCGGCAATT seq5_BACSU 40 7.37e-06 ATGGCAAGGT GTTCAGGTTTTTCTCACGGAGA ACTGTCTAAC seq13_BACSU 35 8.59e-06 CTTGTCTAAA GGGCAGTTTTATAAGTGGTAAA TCACGACATT seq11_BACSU 32 1.07e-05 GTCTTGTAAA AGTATTTTCTTTCTTTGGAAGA AATGCTTATT seq19_BACSU 45 1.15e-05 CTGTAAACGG CTGCTTTCTTCATTATGTATGA ACTTACATTT seq39_BACSU 36 1.24e-05 TTGCTTTAAA GGGCTTGTTTTTGATATGATCA GTATTATATG seq45_BACSU 26 1.64e-05 TGAGGATTTT CGAGAATTTTTCTTATTGAAGA TCCGTGCCAT seq16_BACSU 26 3.75e-05 TCAAAAATTT GTAACGTTTTTATCGTGCGTGA TGAGGAAGGA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GKGCWKTTTTTWTTTTBKRWRA MEME-2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- seq9_BACSU 2.1e-11 52_[+2]_26 seq26_BACSU 4.9e-11 56_[+2]_22 seq48_BACSU 8.6e-08 34_[+2]_44 seq50_BACSU 2.8e-07 61_[+2]_17 seq10_BACSU 4.9e-07 60_[+2]_18 seq21_BACSU 7.4e-07 58_[+2]_20 seq41_BACSU 9e-07 9_[+2]_69 seq6_BACSU 9e-07 50_[+2]_28 seq30_BACSU 1.5e-06 14_[+2]_64 seq44_BACSU 1.8e-06 31_[+2]_47 seq24_BACSU 5.4e-06 35_[+2]_43 seq37_BACSU 5.8e-06 22_[+2]_56 seq5_BACSU 7.4e-06 39_[+2]_39 seq13_BACSU 8.6e-06 34_[+2]_44 seq11_BACSU 1.1e-05 31_[+2]_47 seq19_BACSU 1.2e-05 44_[+2]_34 seq39_BACSU 1.2e-05 35_[+2]_43 seq45_BACSU 1.6e-05 25_[+2]_53 seq16_BACSU 3.7e-05 25_[+2]_53 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GKGCWKTTTTTWTTTTBKRWRA MEME-2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF GKGCWKTTTTTWTTTTBKRWRA width=22 seqs=19 seq9_BACSU ( 53) GGGCTCTTTTTATTTTCGATAA 1 seq26_BACSU ( 57) GGGCTTTTTTTATTTTCTGAAA 1 seq48_BACSU ( 35) GGTCAGTTTTTAATTTGGGATA 1 seq50_BACSU ( 62) GGGCTCTTTTTTGTGTTTGTAA 1 seq10_BACSU ( 61) GTCCGTTTTTTATTTGCCAAAA 1 seq21_BACSU ( 59) GGCCAAGTTTTTCTTTCGCTTA 1 seq41_BACSU ( 10) GTGAGTTTTTTGTTATGTAAAA 1 seq6_BACSU ( 51) AGACGGTTTTTATTTTCCACAA 1 seq30_BACSU ( 15) GGGGATTTTTACATATCGCAAA 1 seq44_BACSU ( 32) GCTCTTTTTTTGTGTTCTATAA 1 seq24_BACSU ( 36) GGGGATTTTTTATTTTTGTCCG 1 seq37_BACSU ( 23) GTGGCCTTTTCGCTTTGTCATA 1 seq5_BACSU ( 40) GTTCAGGTTTTTCTCACGGAGA 1 seq13_BACSU ( 35) GGGCAGTTTTATAAGTGGTAAA 1 seq11_BACSU ( 32) AGTATTTTCTTTCTTTGGAAGA 1 seq19_BACSU ( 45) CTGCTTTCTTCATTATGTATGA 1 seq39_BACSU ( 36) GGGCTTGTTTTTGATATGATCA 1 seq45_BACSU ( 26) CGAGAATTTTTCTTATTGAAGA 1 seq16_BACSU ( 26) GTAACGTTTTTATCGTGCGTGA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GKGCWKTTTTTWTTTTBKRWRA MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 22 n= 3950 bayes= 7.88845 E= 2.8e-006 -164 -57 183 -1089 -1089 -157 151 10 -105 -57 125 -48 -105 201 -8 -1089 17 -57 -49 32 -164 1 25 69 -1089 -1089 -49 152 -1089 -157 -1089 169 -1089 -157 -1089 169 -1089 -1089 -1089 176 -164 -57 -1089 142 36 -57 -49 10 -105 43 -107 84 -164 -157 -207 142 -64 -157 -49 98 -164 -1089 -207 152 -1089 143 73 -48 -1089 1 125 10 53 1 25 -148 68 -57 -1089 32 53 -57 25 -90 153 -1089 -207 -1089 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GKGCWKTTTTTWTTTTBKRWRA MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 22 nsites= 19 E= 2.8e-006 0.105263 0.105263 0.789474 0.000000 0.000000 0.052632 0.631579 0.315789 0.157895 0.105263 0.526316 0.210526 0.157895 0.631579 0.210526 0.000000 0.368421 0.105263 0.157895 0.368421 0.105263 0.157895 0.263158 0.473684 0.000000 0.000000 0.157895 0.842105 0.000000 0.052632 0.000000 0.947368 0.000000 0.052632 0.000000 0.947368 0.000000 0.000000 0.000000 1.000000 0.105263 0.105263 0.000000 0.789474 0.421053 0.105263 0.157895 0.315789 0.157895 0.210526 0.105263 0.526316 0.105263 0.052632 0.052632 0.789474 0.210526 0.052632 0.157895 0.578947 0.105263 0.000000 0.052632 0.842105 0.000000 0.421053 0.368421 0.210526 0.000000 0.157895 0.526316 0.315789 0.473684 0.157895 0.263158 0.105263 0.526316 0.105263 0.000000 0.368421 0.473684 0.105263 0.263158 0.157895 0.947368 0.000000 0.052632 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GKGCWKTTTTTWTTTTBKRWRA MEME-2 regular expression -------------------------------------------------------------------------------- G[GT][GT][CG][AT][TG]TTTTT[AT][TC]T[TA]T[CGT][GT][AG][AT][AG]A -------------------------------------------------------------------------------- Time 4.61 secs. ******************************************************************************** ******************************************************************************** MOTIF CTCGTYCYTTWWKSGG MEME-3 width = 16 sites = 6 llr = 96 E-value = 4.5e-002 ******************************************************************************** -------------------------------------------------------------------------------- Motif CTCGTYCYTTWWKSGG MEME-3 Description -------------------------------------------------------------------------------- Simplified A 22::::::::33:::2 pos.-specific C 7:a::7a5:::::3:: probability G :2:a:::::22257a8 matrix T 27::a3:5a8555::: bits 2.7 * * 2.4 * * 2.1 ** * * 1.9 *** * * * Relative 1.6 *** * * * Entropy 1.3 ******* *** (23.2 bits) 1.1 * ******** **** 0.8 * ******** **** 0.5 ********** **** 0.3 **************** 0.0 ---------------- Multilevel CTCGTCCCTTTTGGGG consensus T T AATC sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTCGTYCYTTWWKSGG MEME-3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- seq9_BACSU 32 3.66e-10 CGCGAGAGCT CTCGTCCCTTTATGGG GATGAGGGCT seq50_BACSU 44 5.63e-09 TGCATTGAGC CACGTCCCTTATTGGG ATGGGCTCTT seq26_BACSU 36 8.79e-09 GATAAGCTTT CTCGTCCCTTATGGGA TGAGAGGGCT seq17_BACSU 50 9.77e-09 TATCGCCGCT CTCGTCCTTTGGGCGG GAGCTTTTTG seq45_BACSU 66 1.48e-07 ATTTGTCAGT AGCGTTCTTTTTGCGG GCAAGCTGCG seq36_BACSU 42 1.97e-07 ATAAAGAACA TTCGTTCTTGTATGGG GTACTTTCTC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTCGTYCYTTWWKSGG MEME-3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- seq9_BACSU 3.7e-10 31_[+3]_53 seq50_BACSU 5.6e-09 43_[+3]_41 seq26_BACSU 8.8e-09 35_[+3]_49 seq17_BACSU 9.8e-09 49_[+3]_35 seq45_BACSU 1.5e-07 65_[+3]_19 seq36_BACSU 2e-07 41_[+3]_43 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTCGTYCYTTWWKSGG MEME-3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF CTCGTYCYTTWWKSGG width=16 seqs=6 seq9_BACSU ( 32) CTCGTCCCTTTATGGG 1 seq50_BACSU ( 44) CACGTCCCTTATTGGG 1 seq26_BACSU ( 36) CTCGTCCCTTATGGGA 1 seq17_BACSU ( 50) CTCGTCCTTTGGGCGG 1 seq45_BACSU ( 66) AGCGTTCTTTTTGCGG 1 seq36_BACSU ( 42) TTCGTTCTTGTATGGG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTCGTYCYTTWWKSGG MEME-3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 4250 bayes= 9.91425 E= 4.5e-002 -97 209 -923 -82 -97 -923 -41 118 -923 267 -923 -923 -923 -923 217 -923 -923 -923 -923 176 -923 209 -923 18 -923 267 -923 -923 -923 167 -923 76 -923 -923 -923 176 -923 -923 -41 150 3 -923 -41 76 3 -923 -41 76 -923 -923 117 76 -923 109 159 -923 -923 -923 217 -923 -97 -923 191 -923 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTCGTYCYTTWWKSGG MEME-3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 6 E= 4.5e-002 0.166667 0.666667 0.000000 0.166667 0.166667 0.000000 0.166667 0.666667 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.666667 0.000000 0.333333 0.000000 1.000000 0.000000 0.000000 0.000000 0.500000 0.000000 0.500000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.166667 0.833333 0.333333 0.000000 0.166667 0.500000 0.333333 0.000000 0.166667 0.500000 0.000000 0.000000 0.500000 0.500000 0.000000 0.333333 0.666667 0.000000 0.000000 0.000000 1.000000 0.000000 0.166667 0.000000 0.833333 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTCGTYCYTTWWKSGG MEME-3 regular expression -------------------------------------------------------------------------------- CTCGT[CT]C[CT]TT[TA][TA][GT][GC]GG -------------------------------------------------------------------------------- Time 6.45 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- seq1_BACSU 3.61e-01 100 seq2_BACSU 6.97e-02 100 seq3_BACSU 6.16e-02 100 seq4_BACSU 4.61e-01 100 seq5_BACSU 2.78e-05 39_[+2(7.37e-06)]_23_[+1(2.78e-05)]_\ 8 seq6_BACSU 2.38e-05 50_[+2(9.01e-07)]_10_[+1(2.78e-05)]_\ 10 seq7_BACSU 1.86e-02 82_[+1(2.78e-05)]_10 seq8_BACSU 2.77e-01 100 seq9_BACSU 1.44e-15 31_[+3(3.66e-10)]_5_[+2(2.09e-11)]_\ 26 seq10_BACSU 2.10e-05 60_[+2(4.87e-07)]_18 seq11_BACSU 3.93e-04 31_[+2(1.07e-05)]_47 seq12_BACSU 1.42e-01 100 seq13_BACSU 3.69e-03 34_[+2(8.59e-06)]_44 seq14_BACSU 9.00e-01 100 seq15_BACSU 1.82e-01 100 seq16_BACSU 1.29e-04 25_[+2(3.75e-05)]_53 seq17_BACSU 2.49e-06 49_[+3(9.77e-09)]_35 seq18_BACSU 9.33e-02 100 seq19_BACSU 1.02e-03 44_[+2(1.15e-05)]_34 seq20_BACSU 1.41e-01 100 seq21_BACSU 1.08e-04 58_[+2(7.37e-07)]_20 seq22_BACSU 4.53e-01 100 seq23_BACSU 7.45e-02 100 seq24_BACSU 1.02e-03 35_[+2(5.39e-06)]_43 seq25_BACSU 4.24e-01 100 seq26_BACSU 8.85e-14 35_[+3(8.79e-09)]_5_[+2(4.85e-11)]_\ 22 seq27_BACSU 6.43e-02 100 seq28_BACSU 2.00e-02 84_[+1(2.78e-05)]_8 seq29_BACSU 9.84e-02 100 seq30_BACSU 1.19e-04 14_[+2(1.46e-06)]_64 seq31_BACSU 5.11e-02 100 seq32_BACSU 3.30e-02 100 seq33_BACSU 1.00e-02 100 seq34_BACSU 2.06e-01 100 seq35_BACSU 2.80e-01 100 seq36_BACSU 9.14e-05 41_[+3(1.97e-07)]_43 seq37_BACSU 7.67e-05 22_[+2(5.83e-06)]_29_[+3(6.02e-05)]_\ 11 seq38_BACSU 8.97e-02 100 seq39_BACSU 1.43e-03 35_[+2(1.24e-05)]_43 seq40_BACSU 3.13e-01 100 seq41_BACSU 1.58e-04 9_[+2(9.01e-07)]_69 seq42_BACSU 4.70e-01 100 seq43_BACSU 2.21e-01 100 seq44_BACSU 1.35e-05 31_[+2(1.76e-06)]_25_[+1(2.78e-05)]_\ 14 seq45_BACSU 1.34e-06 25_[+2(1.64e-05)]_18_[+3(1.48e-07)]_\ 19 seq46_BACSU 2.93e-01 100 seq47_BACSU 1.28e-02 100 seq48_BACSU 7.10e-05 34_[+2(8.56e-08)]_44 seq49_BACSU 1.77e-01 100 seq50_BACSU 1.43e-11 43_[+3(5.63e-09)]_2_[+2(2.82e-07)]_\ 1_[+1(2.78e-05)]_8 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (3) found. ******************************************************************************** CPU: kodomo ********************************************************************************