******************************************************************************** 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= household_promoters.fasta CONTROL SEQUENCES= --none-- ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ promoter_1 1.0000 150 promoter_2 1.0000 150 promoter_3 1.0000 150 promoter_4 1.0000 150 promoter_5 1.0000 150 promoter_6 1.0000 150 promoter_7 1.0000 150 promoter_8 1.0000 150 promoter_9 1.0000 150 promoter_10 1.0000 150 promoter_11 1.0000 150 promoter_12 1.0000 150 promoter_13 1.0000 150 promoter_14 1.0000 150 promoter_15 1.0000 150 promoter_16 1.0000 150 promoter_17 1.0000 150 promoter_18 1.0000 150 promoter_19 1.0000 150 promoter_20 1.0000 150 promoter_21 1.0000 150 promoter_22 1.0000 150 promoter_23 1.0000 150 promoter_24 1.0000 150 promoter_25 1.0000 150 promoter_26 1.0000 150 promoter_27 1.0000 150 promoter_28 1.0000 150 promoter_29 1.0000 150 promoter_30 1.0000 150 promoter_31 1.0000 150 promoter_32 1.0000 150 promoter_33 1.0000 150 promoter_34 1.0000 150 promoter_35 1.0000 150 promoter_36 1.0000 150 promoter_37 1.0000 150 promoter_38 1.0000 150 promoter_39 1.0000 150 promoter_40 1.0000 150 promoter_41 1.0000 150 promoter_42 1.0000 150 promoter_43 1.0000 150 promoter_44 1.0000 150 promoter_45 1.0000 150 promoter_46 1.0000 150 promoter_47 1.0000 150 promoter_48 1.0000 150 promoter_49 1.0000 150 promoter_50 1.0000 150 ******************************************************************************** ******************************************************************************** COMMAND LINE SUMMARY ******************************************************************************** This information can also be useful in the event you wish to report a problem with the MEME software. command: meme household_promoters.fasta -dna -oc . -nostatus -time 14400 -mod zoops -nmotifs 3 -minw 7 -maxw 9 -objfun classic -minsites 50 -maxsites 50 -markov_order 0 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= 7 maxw= 9 nsites: minsites= 50 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= 7500 N= 50 sample: seed= 0 hsfrac= 0 searchsize= 7500 norand= no csites= 1000 Letter frequencies in dataset: A 0.284 C 0.211 G 0.205 T 0.301 Background letter frequencies (from file dataset with add-one prior applied): A 0.284 C 0.21 G 0.205 T 0.301 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF TTCCGGMAD MEME-1 width = 9 sites = 50 llr = 302 E-value = 3.1e-002 ******************************************************************************** -------------------------------------------------------------------------------- Motif TTCCGGMAD MEME-1 Description -------------------------------------------------------------------------------- Simplified A 2:::12583 pos.-specific C ::79::4:: probability G 112187114 matrix T 781::1:13 bits 2.3 2.1 1.8 1.6 * Relative 1.4 ** Entropy 1.1 ***** (8.7 bits) 0.9 ***** * 0.7 ****** * 0.5 ********* 0.2 ********* 0.0 --------- Multilevel TTCCGGAAG consensus G C T sequence A -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTCCGGMAD MEME-1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------- promoter_50 93 2.05e-06 GATAAAGAGT TTCCGGCAG TGTTTTCGGG promoter_39 36 4.83e-06 AAAAAAACGC TTCCGGAAG GCTATGTACA promoter_17 113 1.07e-05 CCGGTCATGT TTCCGGCAT CCTTACCAAA promoter_36 28 1.86e-05 TAACGCTAAA TTCCGGAAT AACCGCAAAC promoter_11 32 1.86e-05 AAGGCTTTTC TTCCGGAAA AATTATGTTG promoter_10 53 2.26e-05 ACGGACTTCC TTGCGGCAG CAAGAGAGAG promoter_26 18 3.08e-05 GACGAGTGGC TTGCGGAAG GATCGATGCT promoter_5 31 3.08e-05 GGTGGCTCGC ATCCGGAAG AAATCGCCTA promoter_24 93 4.66e-05 GCGCGTCGCT TTCCGAAAG GTTCAGGGGA promoter_18 5 4.66e-05 TGAA GTCCGGAAG GGGTGTTCCC promoter_42 52 5.79e-05 TTTTACTCCG TTGCGGCAA CATTCCGTTT promoter_15 30 1.08e-04 GCGGGTGATT TTTCGGCAG TGTCAATCTG promoter_28 89 1.14e-04 ATTGTACTAT TTCGGGCAG AGGTCTGCTG promoter_13 32 1.14e-04 TATCTCACTT TTTCGGAAG GCTTTATTTT promoter_7 53 1.47e-04 ATTGTCATTT TTCCGAAAT GATGATGCCG promoter_8 114 1.63e-04 TCGGAAAGCA ATCCGGCGG CGCAGCATGA promoter_35 137 1.87e-04 TTATCCATTT TTCCAGCAA TATCC promoter_31 65 1.87e-04 GAAGAAATTC ATCCGGAGG GCCTTAGGAA promoter_30 81 2.03e-04 CTCCCATTAA TTCCAGAAT AACTTAAATT promoter_19 117 2.38e-04 AAACTTTATT TTTCGGAAA AGTCCAGTTA promoter_34 88 3.38e-04 TTTTTCGTTG TTCCGGTAA CCGACCGCAA promoter_21 96 3.38e-04 AAGTCCGGAT TTCCGGTAA CCTGATCATA promoter_44 45 3.99e-04 GAAAAACAGA TGCCGGCGA AAAGCTTTGA promoter_49 118 4.84e-04 TCAGGTTTAC ATCCGACAA CGCTCAACAC promoter_45 78 5.47e-04 GCTTTGAACG CTCCGGCAA TAGTGTAAAT promoter_37 78 5.47e-04 AGCGGGATGG TTCGGGAGG TTGCAGCCTG promoter_29 142 6.04e-04 ATTCAGAAAA ATCCGTCAG promoter_38 76 6.78e-04 ATTCAGACTT TTCAGGCAA TCCGTTCGGA promoter_3 139 6.78e-04 CCCAGTCACA TTCCGAGAT ATT promoter_2 44 6.78e-04 GCAAAGCGCT TGCCGTCAG CGTCTATCAC promoter_40 74 7.54e-04 AATGTCCTGA TTCAGGAAT GGAAAGACAG promoter_33 124 7.54e-04 TATGCCATCA TGGCGGAGG AAATGGTAAC promoter_20 45 7.54e-04 GATTTAAAAT TCCCGGAAT ATCACCGTTA promoter_43 40 8.03e-04 CGGTTCTTCC AGCCGGGAG TAGTGCAGAA promoter_41 95 8.03e-04 TGCAAAATCC TTCCTGAAG CCTTATATTC promoter_14 5 8.03e-04 GGCA GTCCGACAA TCCCGCAGCG promoter_22 25 8.60e-04 GTGGCCGAGG ATCGGGCAT CCGCCTGTCC promoter_32 45 1.27e-03 CATCCGTGGA TTGCGGATT TTAGAAGTCA promoter_23 75 1.38e-03 ATGCCGAAAC TTCCATAAG AAACCTGACA promoter_6 87 1.47e-03 TTTAAGAAGT TGGCGGGAT TTTATACATT promoter_1 44 1.54e-03 TCTGTGGATT TTTCGGATG TTAAATTGTT promoter_27 4 1.69e-03 AAT AGCCGACAA CCGCTTGCAA promoter_12 50 1.97e-03 GGGGTGTAGA GTGCGGGAT CAAAATTTTT promoter_46 57 2.17e-03 GCTTTTGCTT ATGCAGAAA AGCCTGCCTG promoter_25 61 2.33e-03 AAAAATACCT GTGCGACAT CCTGATTGCT promoter_9 100 2.33e-03 CGCTTTCATT TTCCATAAT AATTTTTGTA promoter_4 34 2.88e-03 TAACCCGCGC TTCGGGATT ATACGCTTCA promoter_47 79 3.08e-03 TTTCACCCTT TGCCAACAA GAAGCCTCAA promoter_16 16 4.38e-03 GCCCGACCCC TTTCAGCGT GGTCAATGAC promoter_48 2 1.35e-02 G TTGCCAAGG CTTCTCAGGG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTCCGGMAD MEME-1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- promoter_50 2.1e-06 92_[+1]_49 promoter_39 4.8e-06 35_[+1]_106 promoter_17 1.1e-05 112_[+1]_29 promoter_36 1.9e-05 27_[+1]_114 promoter_11 1.9e-05 31_[+1]_110 promoter_10 2.3e-05 52_[+1]_89 promoter_26 3.1e-05 17_[+1]_124 promoter_5 3.1e-05 30_[+1]_111 promoter_24 4.7e-05 92_[+1]_49 promoter_18 4.7e-05 4_[+1]_137 promoter_42 5.8e-05 51_[+1]_90 promoter_15 0.00011 29_[+1]_112 promoter_28 0.00011 88_[+1]_53 promoter_13 0.00011 31_[+1]_110 promoter_7 0.00015 52_[+1]_89 promoter_8 0.00016 113_[+1]_28 promoter_35 0.00019 136_[+1]_5 promoter_31 0.00019 64_[+1]_77 promoter_30 0.0002 80_[+1]_61 promoter_19 0.00024 116_[+1]_25 promoter_34 0.00034 87_[+1]_54 promoter_21 0.00034 95_[+1]_46 promoter_44 0.0004 44_[+1]_97 promoter_49 0.00048 117_[+1]_24 promoter_45 0.00055 77_[+1]_64 promoter_37 0.00055 77_[+1]_64 promoter_29 0.0006 141_[+1] promoter_38 0.00068 75_[+1]_66 promoter_3 0.00068 138_[+1]_3 promoter_2 0.00068 43_[+1]_98 promoter_40 0.00075 73_[+1]_68 promoter_33 0.00075 123_[+1]_18 promoter_20 0.00075 44_[+1]_97 promoter_43 0.0008 39_[+1]_102 promoter_41 0.0008 94_[+1]_47 promoter_14 0.0008 4_[+1]_137 promoter_22 0.00086 24_[+1]_117 promoter_32 0.0013 44_[+1]_97 promoter_23 0.0014 74_[+1]_67 promoter_6 0.0015 86_[+1]_55 promoter_1 0.0015 43_[+1]_98 promoter_27 0.0017 3_[+1]_138 promoter_12 0.002 49_[+1]_92 promoter_46 0.0022 56_[+1]_85 promoter_25 0.0023 60_[+1]_81 promoter_9 0.0023 99_[+1]_42 promoter_4 0.0029 33_[+1]_108 promoter_47 0.0031 78_[+1]_63 promoter_16 0.0044 15_[+1]_126 promoter_48 0.013 1_[+1]_140 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTCCGGMAD MEME-1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF TTCCGGMAD width=9 seqs=50 promoter_50 ( 93) TTCCGGCAG 1 promoter_39 ( 36) TTCCGGAAG 1 promoter_17 ( 113) TTCCGGCAT 1 promoter_36 ( 28) TTCCGGAAT 1 promoter_11 ( 32) TTCCGGAAA 1 promoter_10 ( 53) TTGCGGCAG 1 promoter_26 ( 18) TTGCGGAAG 1 promoter_5 ( 31) ATCCGGAAG 1 promoter_24 ( 93) TTCCGAAAG 1 promoter_18 ( 5) GTCCGGAAG 1 promoter_42 ( 52) TTGCGGCAA 1 promoter_15 ( 30) TTTCGGCAG 1 promoter_28 ( 89) TTCGGGCAG 1 promoter_13 ( 32) TTTCGGAAG 1 promoter_7 ( 53) TTCCGAAAT 1 promoter_8 ( 114) ATCCGGCGG 1 promoter_35 ( 137) TTCCAGCAA 1 promoter_31 ( 65) ATCCGGAGG 1 promoter_30 ( 81) TTCCAGAAT 1 promoter_19 ( 117) TTTCGGAAA 1 promoter_34 ( 88) TTCCGGTAA 1 promoter_21 ( 96) TTCCGGTAA 1 promoter_44 ( 45) TGCCGGCGA 1 promoter_49 ( 118) ATCCGACAA 1 promoter_45 ( 78) CTCCGGCAA 1 promoter_37 ( 78) TTCGGGAGG 1 promoter_29 ( 142) ATCCGTCAG 1 promoter_38 ( 76) TTCAGGCAA 1 promoter_3 ( 139) TTCCGAGAT 1 promoter_2 ( 44) TGCCGTCAG 1 promoter_40 ( 74) TTCAGGAAT 1 promoter_33 ( 124) TGGCGGAGG 1 promoter_20 ( 45) TCCCGGAAT 1 promoter_43 ( 40) AGCCGGGAG 1 promoter_41 ( 95) TTCCTGAAG 1 promoter_14 ( 5) GTCCGACAA 1 promoter_22 ( 25) ATCGGGCAT 1 promoter_32 ( 45) TTGCGGATT 1 promoter_23 ( 75) TTCCATAAG 1 promoter_6 ( 87) TGGCGGGAT 1 promoter_1 ( 44) TTTCGGATG 1 promoter_27 ( 4) AGCCGACAA 1 promoter_12 ( 50) GTGCGGGAT 1 promoter_46 ( 57) ATGCAGAAA 1 promoter_25 ( 61) GTGCGACAT 1 promoter_9 ( 100) TTCCATAAT 1 promoter_4 ( 34) TTCGGGATT 1 promoter_47 ( 79) TGCCAACAA 1 promoter_16 ( 16) TTTCAGCGT 1 promoter_48 ( 2) TTGCCAAGG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTCCGGMAD MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 9 n= 7100 bayes= 7.13955 E= 3.1e-002 -66 -339 -135 126 -1229 -339 -55 148 -1229 173 -3 -159 -283 206 -135 -1229 -102 -339 200 -391 -66 -1229 185 -191 76 93 -135 -291 149 -1229 -55 -232 -2 -1229 104 0 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTCCGGMAD MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 9 nsites= 50 E= 3.1e-002 0.180000 0.020000 0.080000 0.720000 0.000000 0.020000 0.140000 0.840000 0.000000 0.700000 0.200000 0.100000 0.040000 0.880000 0.080000 0.000000 0.140000 0.020000 0.820000 0.020000 0.180000 0.000000 0.740000 0.080000 0.480000 0.400000 0.080000 0.040000 0.800000 0.000000 0.140000 0.060000 0.280000 0.000000 0.420000 0.300000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTCCGGMAD MEME-1 regular expression -------------------------------------------------------------------------------- TT[CG]CGG[AC]A[GTA] -------------------------------------------------------------------------------- Time 0.74 secs. ******************************************************************************** ******************************************************************************** MOTIF RAAAAABS MEME-2 width = 8 sites = 50 llr = 284 E-value = 9.1e+003 ******************************************************************************** -------------------------------------------------------------------------------- Motif RAAAAABS MEME-2 Description -------------------------------------------------------------------------------- Simplified A 39a877:2 pos.-specific C :1:2:145 probability G 6:::3134 matrix T ::::::3: bits 2.3 2.1 1.8 1.6 * Relative 1.4 ** Entropy 1.1 **** (8.2 bits) 0.9 ****** 0.7 ****** * 0.5 ******** 0.2 ******** 0.0 -------- Multilevel GAAAAACC consensus A G TG sequence G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RAAAAABS MEME-2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- promoter_30 135 1.67e-05 CAGCGAACAG GAAAAACC CGGACATC promoter_31 28 3.30e-05 ACAAGCCGAT GAAAAACG ACTTCGAACA promoter_28 31 4.93e-05 GCTCGTTCAG GAAAAAGC CTGTAAACAG promoter_14 109 4.93e-05 ATTAAGTTTG GAAAAAGC AAATTTATTT promoter_34 15 8.53e-05 GACCAGAAGC GAAAAATC CCGTTCGAGA promoter_20 24 8.53e-05 TGACATGATG GAAAAATC ACTGATTTAA promoter_47 131 1.71e-04 AATGAAAGCA AAAAAACC CGGACAAAAA promoter_41 72 1.71e-04 AAGAGAAACA AAAAAACC GAACTTGCAA promoter_11 140 1.71e-04 CAGCAACAAG AAAAAACC TCT promoter_10 142 1.71e-04 CTGTTTTTTA GAAAGAGC T promoter_8 8 1.71e-04 TTACCGA AAAAAACC GGTCAGCCCC promoter_6 142 1.71e-04 TATTACACGG AAAAAACC T promoter_4 143 2.01e-04 CACCTTTTCT GAACAACC promoter_49 84 2.70e-04 CTTTTCTTTC AAAAAACG TAAAACAGTA promoter_48 125 2.70e-04 CATCAATAAA GAAAAACA CAATACCGGG promoter_44 35 2.70e-04 AAAAAAAGTG GAAAAACA GATGCCGGCG promoter_39 27 2.70e-04 TGTTTCACCA AAAAAACG CTTCCGGAAG promoter_18 37 2.70e-04 CGGGGTCTGA AAAAAACG TTTTTTGCTA promoter_13 58 3.33e-04 TTTTTTACAG GAAAGATG CAGGAAGAAC promoter_32 4 4.07e-04 GGG AAAAGACC AGCTTTGTTG promoter_24 15 4.07e-04 AAAGATATAA AAAAAATC GAATTCAAGT promoter_22 58 4.07e-04 GCAGGCGGGC GAACAAGC GGATGGAGCA promoter_38 121 4.75e-04 TTATTTAAGA GAAAAAGA TATGTATAGA promoter_29 88 5.14e-04 CACGTATACC GAACAATC TCAATCCGCG promoter_50 67 6.49e-04 TTATCGAATT AAAAAATG ACCTTAAGGA promoter_43 56 6.49e-04 GAGTAGTGCA GAAAGACA GATTATTTGT promoter_40 84 6.49e-04 TTCAGGAATG GAAAGACA GAATCGACCG promoter_36 135 6.49e-04 AAGATACGTG AAAAGACG ATAAGACC promoter_33 25 6.49e-04 TAAGTTATAA AAAAAATG AGGAATGTCC promoter_25 50 6.49e-04 TCAACTGCGT GAAAAATA CCTGTGCGAC promoter_37 26 7.03e-04 TTTGTTCGGC GAAAAGGG GGAGCAGATG promoter_26 130 9.30e-04 CAAAGCGGTG GAAAACTG AACACATTGC promoter_15 64 9.30e-04 TTGTACCTTC AAAAAACA CCGACTTTTT promoter_1 74 9.30e-04 TTTATCCACC GAAAACTG TAACTTGTGA promoter_12 36 1.17e-03 GGTTCCCGGT GAAAGGGG TGTAGAGTGC promoter_16 51 1.55e-03 ACGGCCATAG GAAAGCTG TTGTATATCG promoter_21 133 1.78e-03 TTGCGTTGAC AAAAACGG AATATGTACC promoter_19 3 1.94e-03 AG GCAAAAGG GTCTTGTAAG promoter_9 2 2.37e-03 T GAACGGGC TGTAAATATA promoter_7 76 2.63e-03 ATGCCGAGGG GAACGGTC TGCGCAATGC promoter_23 140 2.84e-03 AGACATAGCG GAACGCTC TAT promoter_5 126 2.84e-03 GATTTCACCA TAAAAATC CTATCCACAC promoter_3 60 3.02e-03 GAAACGGGAT GAACGCGG CATGAGTGGG promoter_2 34 3.35e-03 TTATATGACA GCAAAGCG CTTGCCGTCA promoter_42 105 3.59e-03 GCATTGTCCT GAGAAGCC GAAGGGCAGG promoter_27 137 5.26e-03 CCCATATAAA GAACAAAG CCTGTT promoter_35 21 6.12e-03 CTGGTATCGC GAGAGAGA TATGCTGTAA promoter_45 7 7.05e-03 ACTGGT ACAAACTC TTCGCCATTT promoter_46 37 9.13e-03 CATAGCGGTA TAACAGGC AGGCTTTTGC promoter_17 92 9.13e-03 CAGACGGAGG GGAAGATA CTCCCGGTCA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RAAAAABS MEME-2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- promoter_30 1.7e-05 134_[+2]_8 promoter_31 3.3e-05 27_[+2]_115 promoter_28 4.9e-05 30_[+2]_112 promoter_14 4.9e-05 108_[+2]_34 promoter_34 8.5e-05 14_[+2]_128 promoter_20 8.5e-05 23_[+2]_119 promoter_47 0.00017 130_[+2]_12 promoter_41 0.00017 71_[+2]_71 promoter_11 0.00017 139_[+2]_3 promoter_10 0.00017 141_[+2]_1 promoter_8 0.00017 7_[+2]_135 promoter_6 0.00017 141_[+2]_1 promoter_4 0.0002 142_[+2] promoter_49 0.00027 83_[+2]_59 promoter_48 0.00027 124_[+2]_18 promoter_44 0.00027 34_[+2]_108 promoter_39 0.00027 26_[+2]_116 promoter_18 0.00027 36_[+2]_106 promoter_13 0.00033 57_[+2]_85 promoter_32 0.00041 3_[+2]_139 promoter_24 0.00041 14_[+2]_128 promoter_22 0.00041 57_[+2]_85 promoter_38 0.00048 120_[+2]_22 promoter_29 0.00051 87_[+2]_55 promoter_50 0.00065 66_[+2]_76 promoter_43 0.00065 55_[+2]_87 promoter_40 0.00065 83_[+2]_59 promoter_36 0.00065 134_[+2]_8 promoter_33 0.00065 24_[+2]_118 promoter_25 0.00065 49_[+2]_93 promoter_37 0.0007 25_[+2]_117 promoter_26 0.00093 129_[+2]_13 promoter_15 0.00093 63_[+2]_79 promoter_1 0.00093 73_[+2]_69 promoter_12 0.0012 35_[+2]_107 promoter_16 0.0015 50_[+2]_92 promoter_21 0.0018 132_[+2]_10 promoter_19 0.0019 2_[+2]_140 promoter_9 0.0024 1_[+2]_141 promoter_7 0.0026 75_[+2]_67 promoter_23 0.0028 139_[+2]_3 promoter_5 0.0028 125_[+2]_17 promoter_3 0.003 59_[+2]_83 promoter_2 0.0034 33_[+2]_109 promoter_42 0.0036 104_[+2]_38 promoter_27 0.0053 136_[+2]_6 promoter_35 0.0061 20_[+2]_122 promoter_45 0.007 6_[+2]_136 promoter_46 0.0091 36_[+2]_106 promoter_17 0.0091 91_[+2]_51 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RAAAAABS MEME-2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF RAAAAABS width=8 seqs=50 promoter_30 ( 135) GAAAAACC 1 promoter_31 ( 28) GAAAAACG 1 promoter_28 ( 31) GAAAAAGC 1 promoter_14 ( 109) GAAAAAGC 1 promoter_34 ( 15) GAAAAATC 1 promoter_20 ( 24) GAAAAATC 1 promoter_47 ( 131) AAAAAACC 1 promoter_41 ( 72) AAAAAACC 1 promoter_11 ( 140) AAAAAACC 1 promoter_10 ( 142) GAAAGAGC 1 promoter_8 ( 8) AAAAAACC 1 promoter_6 ( 142) AAAAAACC 1 promoter_4 ( 143) GAACAACC 1 promoter_49 ( 84) AAAAAACG 1 promoter_48 ( 125) GAAAAACA 1 promoter_44 ( 35) GAAAAACA 1 promoter_39 ( 27) AAAAAACG 1 promoter_18 ( 37) AAAAAACG 1 promoter_13 ( 58) GAAAGATG 1 promoter_32 ( 4) AAAAGACC 1 promoter_24 ( 15) AAAAAATC 1 promoter_22 ( 58) GAACAAGC 1 promoter_38 ( 121) GAAAAAGA 1 promoter_29 ( 88) GAACAATC 1 promoter_50 ( 67) AAAAAATG 1 promoter_43 ( 56) GAAAGACA 1 promoter_40 ( 84) GAAAGACA 1 promoter_36 ( 135) AAAAGACG 1 promoter_33 ( 25) AAAAAATG 1 promoter_25 ( 50) GAAAAATA 1 promoter_37 ( 26) GAAAAGGG 1 promoter_26 ( 130) GAAAACTG 1 promoter_15 ( 64) AAAAAACA 1 promoter_1 ( 74) GAAAACTG 1 promoter_12 ( 36) GAAAGGGG 1 promoter_16 ( 51) GAAAGCTG 1 promoter_21 ( 133) AAAAACGG 1 promoter_19 ( 3) GCAAAAGG 1 promoter_9 ( 2) GAACGGGC 1 promoter_7 ( 76) GAACGGTC 1 promoter_23 ( 140) GAACGCTC 1 promoter_5 ( 126) TAAAAATC 1 promoter_3 ( 60) GAACGCGG 1 promoter_2 ( 34) GCAAAGCG 1 promoter_42 ( 105) GAGAAGCC 1 promoter_27 ( 137) GAACAAAG 1 promoter_35 ( 21) GAGAGAGA 1 promoter_45 ( 7) ACAAACTC 1 promoter_46 ( 37) TAACAGGC 1 promoter_17 ( 92) GGAAGATA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RAAAAABS MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 7150 bayes= 7.14975 E= 9.1e+003 17 -1229 164 -291 170 -181 -335 -1229 176 -1229 -235 -1229 153 -23 -1229 -1229 134 -1229 45 -1229 134 -59 -55 -1229 -382 93 34 9 -66 113 81 -1229 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RAAAAABS MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 50 E= 9.1e+003 0.320000 0.000000 0.640000 0.040000 0.920000 0.060000 0.020000 0.000000 0.960000 0.000000 0.040000 0.000000 0.820000 0.180000 0.000000 0.000000 0.720000 0.000000 0.280000 0.000000 0.720000 0.140000 0.140000 0.000000 0.020000 0.400000 0.260000 0.320000 0.180000 0.460000 0.360000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RAAAAABS MEME-2 regular expression -------------------------------------------------------------------------------- [GA]AAA[AG]A[CTG][CG] -------------------------------------------------------------------------------- Time 1.44 secs. ******************************************************************************** ******************************************************************************** MOTIF TTWTTTT MEME-3 width = 7 sites = 50 llr = 268 E-value = 6.6e+007 ******************************************************************************** -------------------------------------------------------------------------------- Motif TTWTTTT MEME-3 Description -------------------------------------------------------------------------------- Simplified A 2:5:1:: pos.-specific C :::3::: probability G ::1:1:: matrix T 8a477aa bits 2.3 2.1 1.8 * 1.6 * ** Relative 1.4 * ** Entropy 1.1 * ** (7.7 bits) 0.9 ** * ** 0.7 ** **** 0.5 ******* 0.2 ******* 0.0 ------- Multilevel TTATTTT consensus TC sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTWTTTT MEME-3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------- promoter_48 100 2.11e-04 ACGGCATTAG TTATTTT ACAAATCGCA promoter_47 112 2.11e-04 AACATATGCT TTATTTT TCAATGAAAG promoter_42 38 2.11e-04 TAACTTCATA TTATTTT TACTCCGTTG promoter_39 144 2.11e-04 GTCAGAGTAT TTATTTT promoter_36 63 2.11e-04 ACAGGCAGTT TTATTTT TAACGAAATT promoter_16 98 2.11e-04 AGCACCCTTA TTATTTT ATTGCAGGTC promoter_14 121 2.11e-04 AAAAGCAAAT TTATTTT ATAAAATTAC promoter_3 117 2.11e-04 ATCTTGAGGT TTATTTT GTTCACCCAG promoter_2 106 2.11e-04 TGTAATAAAT TTATTTT AACAACTATG promoter_45 59 4.35e-04 TCGGTGTAAC TTTTTTT ATGCTTTGAA promoter_43 113 4.35e-04 GGTCCAGAGC TTTTTTT GTTTTCTTCA promoter_34 123 4.35e-04 GATCGGTTGC TTTTTTT GTACTTTCCT promoter_33 46 4.35e-04 AATGTCCAGT TTTTTTT ATAAAAAATC promoter_31 90 4.35e-04 GGAAATCATC TTTTTTT GCCATTTTCC promoter_25 143 4.35e-04 CCGCCAACCA TTTTTTT C promoter_15 77 4.35e-04 AAACACCGAC TTTTTTT AAATTCCGTG promoter_13 47 4.35e-04 GAAGGCTTTA TTTTTTT ACAGGAAAGA promoter_10 88 4.35e-04 AATTGTTTCT TTTTTTT CTTTGGATTT promoter_9 54 4.35e-04 TGAATCCTGC TTTTTTT TGATCTTTCT promoter_1 127 4.35e-04 TTCCCCTCGT TTTTTTT ACTAATTCTA promoter_24 139 5.82e-04 CCATTTCAAG TTACTTT GAACA promoter_49 76 7.39e-04 TCCTCATTCT TTTCTTT CAAAAAACGT promoter_46 13 7.39e-04 TTAAGAAGGT TTTCTTT TTTGTCACAT promoter_32 119 7.39e-04 AAGCAGGCGG TTTCTTT CCCTTTTACT promoter_17 57 7.39e-04 ATTTTACGTG TTTCTTT GATGCTATGG promoter_4 93 8.91e-04 CTTATATTCT TTGTTTT ATCTATTGAA promoter_35 121 1.09e-03 ATAGCTCGAT ATATTTT TATCCATTTT promoter_30 64 1.09e-03 GGTGTCGATG ATATTTT CTCCCATTAA promoter_19 92 1.09e-03 ATTAAATGAA ATATTTT ACATTGATAA promoter_18 69 1.09e-03 AGCTGAAATG ATATTTT ATCGTTTTGT promoter_50 15 1.30e-03 AGAAGTGCTA ATTTTTT CGGTAAGGTC promoter_41 106 1.50e-03 TCCTGAAGCC TTATATT CATGCCTCTT promoter_40 45 1.50e-03 GCCTTTTTCA TTATATT CGAAGTCCTG promoter_20 76 1.50e-03 GATAATAGAC TTATATT CTGAAAAGAA promoter_23 44 1.82e-03 TTTATCATAT TTTTATT ATTATACTAA promoter_12 2 1.82e-03 C TTTTATT CTCCCGTCTT promoter_11 43 1.96e-03 TCCGGAAAAA TTATGTT GGCATCGGGA promoter_37 15 2.25e-03 ATGCTGTCCG TTTTGTT CGGCGAAAAG promoter_28 113 2.79e-03 TGCTGGTCGA TTACGTT TGAATGAACT promoter_38 110 3.90e-03 CATTCATCAC TTTATTT AAGAGAAAAA promoter_29 109 4.00e-03 ATCCGCGCTA TTACCTT TGGCTTCACC promoter_7 12 4.00e-03 GGCCAATGCC TTACCTT TAAGGTTCAA promoter_26 32 4.70e-03 GGAAGGATCG ATGCTTT GGCTCCGGAA promoter_21 123 5.73e-03 TAGATGCCCT TTGCGTT GACAAAAACG promoter_6 99 5.73e-03 GCGGGATTTT ATACATT ACGCCCTTAA promoter_44 69 6.03e-03 TTTGAAAATA ATTCATT AGCTTAAAGG promoter_27 51 7.09e-03 AACTATTGGA CTTCTTT AAAATAAATA promoter_5 114 7.49e-03 ATCATAACGT TTGATTT CACCATAAAA promoter_22 96 1.16e-02 GTCGTCAAAT AAATTTT CCGCCGCGGA promoter_8 99 1.16e-02 AGATATCGCG TTGCTTC GGAAAGCAAT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTWTTTT MEME-3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- promoter_48 0.00021 99_[+3]_44 promoter_47 0.00021 111_[+3]_32 promoter_42 0.00021 37_[+3]_106 promoter_39 0.00021 143_[+3] promoter_36 0.00021 62_[+3]_81 promoter_16 0.00021 97_[+3]_46 promoter_14 0.00021 120_[+3]_23 promoter_3 0.00021 116_[+3]_27 promoter_2 0.00021 105_[+3]_38 promoter_45 0.00044 58_[+3]_85 promoter_43 0.00044 112_[+3]_31 promoter_34 0.00044 122_[+3]_21 promoter_33 0.00044 45_[+3]_98 promoter_31 0.00044 89_[+3]_54 promoter_25 0.00044 142_[+3]_1 promoter_15 0.00044 76_[+3]_67 promoter_13 0.00044 46_[+3]_97 promoter_10 0.00044 87_[+3]_56 promoter_9 0.00044 53_[+3]_90 promoter_1 0.00044 126_[+3]_17 promoter_24 0.00058 138_[+3]_5 promoter_49 0.00074 75_[+3]_68 promoter_46 0.00074 12_[+3]_131 promoter_32 0.00074 118_[+3]_25 promoter_17 0.00074 56_[+3]_87 promoter_4 0.00089 92_[+3]_51 promoter_35 0.0011 120_[+3]_23 promoter_30 0.0011 63_[+3]_80 promoter_19 0.0011 91_[+3]_52 promoter_18 0.0011 68_[+3]_75 promoter_50 0.0013 14_[+3]_129 promoter_41 0.0015 105_[+3]_38 promoter_40 0.0015 44_[+3]_99 promoter_20 0.0015 75_[+3]_68 promoter_23 0.0018 43_[+3]_100 promoter_12 0.0018 1_[+3]_142 promoter_11 0.002 42_[+3]_101 promoter_37 0.0023 14_[+3]_129 promoter_28 0.0028 112_[+3]_31 promoter_38 0.0039 109_[+3]_34 promoter_29 0.004 108_[+3]_35 promoter_7 0.004 11_[+3]_132 promoter_26 0.0047 31_[+3]_112 promoter_21 0.0057 122_[+3]_21 promoter_6 0.0057 98_[+3]_45 promoter_44 0.006 68_[+3]_75 promoter_27 0.0071 50_[+3]_93 promoter_5 0.0075 113_[+3]_30 promoter_22 0.012 95_[+3]_48 promoter_8 0.012 98_[+3]_45 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTWTTTT MEME-3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF TTWTTTT width=7 seqs=50 promoter_48 ( 100) TTATTTT 1 promoter_47 ( 112) TTATTTT 1 promoter_42 ( 38) TTATTTT 1 promoter_39 ( 144) TTATTTT 1 promoter_36 ( 63) TTATTTT 1 promoter_16 ( 98) TTATTTT 1 promoter_14 ( 121) TTATTTT 1 promoter_3 ( 117) TTATTTT 1 promoter_2 ( 106) TTATTTT 1 promoter_45 ( 59) TTTTTTT 1 promoter_43 ( 113) TTTTTTT 1 promoter_34 ( 123) TTTTTTT 1 promoter_33 ( 46) TTTTTTT 1 promoter_31 ( 90) TTTTTTT 1 promoter_25 ( 143) TTTTTTT 1 promoter_15 ( 77) TTTTTTT 1 promoter_13 ( 47) TTTTTTT 1 promoter_10 ( 88) TTTTTTT 1 promoter_9 ( 54) TTTTTTT 1 promoter_1 ( 127) TTTTTTT 1 promoter_24 ( 139) TTACTTT 1 promoter_49 ( 76) TTTCTTT 1 promoter_46 ( 13) TTTCTTT 1 promoter_32 ( 119) TTTCTTT 1 promoter_17 ( 57) TTTCTTT 1 promoter_4 ( 93) TTGTTTT 1 promoter_35 ( 121) ATATTTT 1 promoter_30 ( 64) ATATTTT 1 promoter_19 ( 92) ATATTTT 1 promoter_18 ( 69) ATATTTT 1 promoter_50 ( 15) ATTTTTT 1 promoter_41 ( 106) TTATATT 1 promoter_40 ( 45) TTATATT 1 promoter_20 ( 76) TTATATT 1 promoter_23 ( 44) TTTTATT 1 promoter_12 ( 2) TTTTATT 1 promoter_11 ( 43) TTATGTT 1 promoter_37 ( 15) TTTTGTT 1 promoter_28 ( 113) TTACGTT 1 promoter_38 ( 110) TTTATTT 1 promoter_29 ( 109) TTACCTT 1 promoter_7 ( 12) TTACCTT 1 promoter_26 ( 32) ATGCTTT 1 promoter_21 ( 123) TTGCGTT 1 promoter_6 ( 99) ATACATT 1 promoter_44 ( 69) ATTCATT 1 promoter_27 ( 51) CTTCTTT 1 promoter_5 ( 114) TTGATTT 1 promoter_22 ( 96) AAATTTT 1 promoter_8 ( 99) TTGCTTC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTWTTTT MEME-3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 7 n= 7200 bayes= 7.15987 E= 6.6e+007 -66 -339 -1229 141 -382 -1229 -1229 170 70 -1229 -103 55 -283 41 -1229 118 -102 -239 -135 130 -1229 -1229 -1229 173 -1229 -339 -1229 170 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTWTTTT MEME-3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 7 nsites= 50 E= 6.6e+007 0.180000 0.020000 0.000000 0.800000 0.020000 0.000000 0.000000 0.980000 0.460000 0.000000 0.100000 0.440000 0.040000 0.280000 0.000000 0.680000 0.140000 0.040000 0.080000 0.740000 0.000000 0.000000 0.000000 1.000000 0.000000 0.020000 0.000000 0.980000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTWTTTT MEME-3 regular expression -------------------------------------------------------------------------------- TT[AT][TC]TTT -------------------------------------------------------------------------------- Time 2.08 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- promoter_1 4.27e-02 150 promoter_2 3.29e-02 150 promoter_3 3.10e-02 150 promoter_4 3.52e-02 150 promoter_5 3.08e-02 30_[+1(3.08e-05)]_111 promoter_6 6.37e-02 150 promoter_7 6.84e-02 150 promoter_8 1.73e-02 150 promoter_9 6.11e-02 150 promoter_10 4.16e-04 52_[+1(2.26e-05)]_89 promoter_11 1.15e-03 31_[+1(1.86e-05)]_110 promoter_12 1.21e-01 150 promoter_13 1.54e-03 150 promoter_14 1.56e-03 108_[+2(4.93e-05)]_34 promoter_15 5.89e-03 150 promoter_16 6.70e-02 150 promoter_17 5.76e-03 112_[+1(1.07e-05)]_29 promoter_18 2.30e-03 4_[+1(4.66e-05)]_137 promoter_19 4.76e-03 150 promoter_20 1.06e-02 23_[+2(8.53e-05)]_119 promoter_21 1.14e-01 150 promoter_22 1.06e-01 150 promoter_23 1.47e-01 150 promoter_24 1.97e-03 92_[+1(4.66e-05)]_49 promoter_25 4.33e-02 150 promoter_26 8.80e-03 17_[+1(3.08e-05)]_124 promoter_27 5.04e-01 150 promoter_28 2.36e-03 30_[+2(4.93e-05)]_112 promoter_29 1.69e-02 136_[+2(8.53e-05)]_6 promoter_30 7.78e-04 134_[+2(1.67e-05)]_8 promoter_31 6.17e-04 27_[+2(3.30e-05)]_115 promoter_32 3.04e-02 150 promoter_33 1.42e-02 150 promoter_34 2.21e-03 14_[+2(8.53e-05)]_128 promoter_35 5.73e-02 150 promoter_36 5.84e-04 27_[+1(1.86e-05)]_114 promoter_37 5.28e-02 150 promoter_38 6.40e-02 150 promoter_39 8.86e-05 35_[+1(4.83e-06)]_106 promoter_40 4.82e-02 150 promoter_41 1.90e-02 150 promoter_42 5.21e-03 51_[+1(5.79e-05)]_90 promoter_43 2.10e-02 150 promoter_44 3.67e-02 150 promoter_45 4.33e-02 150 promoter_46 3.21e-02 150 promoter_47 1.12e-02 150 promoter_48 3.10e-02 150 promoter_49 1.11e-02 150 promoter_50 3.95e-04 92_[+1(2.05e-06)]_49 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (3) found. ******************************************************************************** CPU: noble-meme.grid.gs.washington.edu ********************************************************************************