******************************************************************************** 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 8 -maxw 50 -objfun classic -minsites 25 -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= 8 maxw= 50 nsites: minsites= 25 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 KYTTBCVGAARGVT MEME-1 width = 14 sites = 32 llr = 265 E-value = 1.3e-003 ******************************************************************************** -------------------------------------------------------------------------------- Motif KYTTBCVGAARGVT MEME-1 Description -------------------------------------------------------------------------------- Simplified A ::2:::31686232 pos.-specific C 26::3a2:22:231 probability G 32::4:49:14542 matrix T 538a3:1:2::1:6 bits 2.3 * 2.1 * 1.8 * * * 1.6 * * * Relative 1.4 * * * Entropy 1.1 ** * * (11.9 bits) 0.9 ** * * * 0.7 *** * **** 0.5 ********** ** 0.2 ************** 0.0 -------------- Multilevel TCTTGCGGAAAGGT consensus GT C A C GCA sequence C T C C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif KYTTBCVGAARGVT MEME-1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------------- promoter_39 34 7.19e-08 CCAAAAAAAC GCTTCCGGAAGGCT ATGTACAATG promoter_26 16 7.19e-08 AAGACGAGTG GCTTGCGGAAGGAT CGATGCTTTG promoter_28 131 1.58e-07 GAATGAACTC TCTTCCCGAAAGGT CGTTTT promoter_24 90 5.62e-07 GCGGCGCGTC GCTTTCCGAAAGGT TCAGGGGAGC promoter_11 30 1.51e-06 ACAAGGCTTT TCTTCCGGAAAAAT TATGTTGGCA promoter_13 30 1.81e-06 CCTATCTCAC TTTTTCGGAAGGCT TTATTTTTTT promoter_19 115 7.90e-06 ATAAACTTTA TTTTTCGGAAAAGT CCAGTTAATC promoter_50 17 1.05e-05 AAGTGCTAAT TTTTTCGGTAAGGT CAAAAGATAG promoter_8 79 1.20e-05 AATCGTCTCT CCTTTCGGAGAGAT ATCGCGTTGC promoter_42 50 2.24e-05 ATTTTTACTC CGTTGCGGCAACAT TCCGTTTGGG promoter_10 51 2.52e-05 TAACGGACTT CCTTGCGGCAGCAA GAGAGAGGCA promoter_17 77 3.18e-05 GCTATGGAAC CCTTGCAGACGGAG GGGAAGATAC promoter_41 93 3.97e-05 CTTGCAAAAT CCTTCCTGAAGCCT TATATTCATG promoter_15 28 3.97e-05 TGGCGGGTGA TTTTTCGGCAGTGT CAATCTGTTT promoter_43 34 4.89e-05 GCCCGCCGGT TCTTCCAGCCGGGA GTAGTGCAGA promoter_5 29 7.90e-05 CAGGTGGCTC GCATCCGGAAGAAA TCGCCTAACG promoter_2 41 7.90e-05 ACAGCAAAGC GCTTGCCGTCAGCG TCTATCACCG promoter_35 135 8.65e-05 TTTTATCCAT TTTTCCAGCAATAT CC promoter_34 86 8.65e-05 TGTTTTTCGT TGTTCCGGTAACCG ACCGCAACGA promoter_25 77 1.13e-04 CATCCTGATT GCTTGCAATAAGCT ATATTCTTGT promoter_7 50 1.23e-04 GTGATTGTCA TTTTTCCGAAATGA TGATGCCGAG promoter_14 52 1.33e-04 GTGAAGAGGT GTTTGCAAAAGCGT GCCCTGTCGG promoter_37 95 1.44e-04 GGTTGCAGCC TGTTGCCGCAGTGG CGAGAGGTTC promoter_31 63 1.69e-04 AGGAAGAAAT TCATCCGGAGGGCC TTAGGAAATC promoter_33 98 2.12e-04 TCATACGGCT GGTTGCCGACCGGT CATATGCCAT promoter_23 63 2.12e-04 TATACTAAAA GCATGCCGAAACTT CCATAAGAAA promoter_29 130 2.44e-04 TTCACCCGAA CGATTCAGAAAAAT CCGTCAG promoter_21 94 2.80e-04 CGAAGTCCGG ATTTCCGGTAACCT GATCATAGAT promoter_49 78 2.99e-04 CTCATTCTTT TCTTTCAAAAAACG TAAAACAGTA promoter_46 55 2.99e-04 AGGCTTTTGC TTATGCAGAAAAGC CTGCCTGTTC promoter_44 104 3.87e-04 ATGTGTCCGG TCATGCTGACAGAA GATACAATTA promoter_16 14 4.91e-04 CGGCCCGACC CCTTTCAGCGTGGT CAATGACGAT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif KYTTBCVGAARGVT MEME-1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- promoter_39 7.2e-08 33_[+1]_103 promoter_26 7.2e-08 15_[+1]_121 promoter_28 1.6e-07 130_[+1]_6 promoter_24 5.6e-07 89_[+1]_47 promoter_11 1.5e-06 29_[+1]_107 promoter_13 1.8e-06 29_[+1]_107 promoter_19 7.9e-06 114_[+1]_22 promoter_50 1e-05 16_[+1]_120 promoter_8 1.2e-05 78_[+1]_58 promoter_42 2.2e-05 49_[+1]_87 promoter_10 2.5e-05 50_[+1]_86 promoter_17 3.2e-05 76_[+1]_60 promoter_41 4e-05 92_[+1]_44 promoter_15 4e-05 27_[+1]_109 promoter_43 4.9e-05 33_[+1]_103 promoter_5 7.9e-05 28_[+1]_108 promoter_2 7.9e-05 40_[+1]_96 promoter_35 8.6e-05 134_[+1]_2 promoter_34 8.6e-05 85_[+1]_51 promoter_25 0.00011 76_[+1]_60 promoter_7 0.00012 49_[+1]_87 promoter_14 0.00013 51_[+1]_85 promoter_37 0.00014 94_[+1]_42 promoter_31 0.00017 62_[+1]_74 promoter_33 0.00021 97_[+1]_39 promoter_23 0.00021 62_[+1]_74 promoter_29 0.00024 129_[+1]_7 promoter_21 0.00028 93_[+1]_43 promoter_49 0.0003 77_[+1]_59 promoter_46 0.0003 54_[+1]_82 promoter_44 0.00039 103_[+1]_33 promoter_16 0.00049 13_[+1]_123 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif KYTTBCVGAARGVT MEME-1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF KYTTBCVGAARGVT width=14 seqs=32 promoter_39 ( 34) GCTTCCGGAAGGCT 1 promoter_26 ( 16) GCTTGCGGAAGGAT 1 promoter_28 ( 131) TCTTCCCGAAAGGT 1 promoter_24 ( 90) GCTTTCCGAAAGGT 1 promoter_11 ( 30) TCTTCCGGAAAAAT 1 promoter_13 ( 30) TTTTTCGGAAGGCT 1 promoter_19 ( 115) TTTTTCGGAAAAGT 1 promoter_50 ( 17) TTTTTCGGTAAGGT 1 promoter_8 ( 79) CCTTTCGGAGAGAT 1 promoter_42 ( 50) CGTTGCGGCAACAT 1 promoter_10 ( 51) CCTTGCGGCAGCAA 1 promoter_17 ( 77) CCTTGCAGACGGAG 1 promoter_41 ( 93) CCTTCCTGAAGCCT 1 promoter_15 ( 28) TTTTTCGGCAGTGT 1 promoter_43 ( 34) TCTTCCAGCCGGGA 1 promoter_5 ( 29) GCATCCGGAAGAAA 1 promoter_2 ( 41) GCTTGCCGTCAGCG 1 promoter_35 ( 135) TTTTCCAGCAATAT 1 promoter_34 ( 86) TGTTCCGGTAACCG 1 promoter_25 ( 77) GCTTGCAATAAGCT 1 promoter_7 ( 50) TTTTTCCGAAATGA 1 promoter_14 ( 52) GTTTGCAAAAGCGT 1 promoter_37 ( 95) TGTTGCCGCAGTGG 1 promoter_31 ( 63) TCATCCGGAGGGCC 1 promoter_33 ( 98) GGTTGCCGACCGGT 1 promoter_23 ( 63) GCATGCCGAAACTT 1 promoter_29 ( 130) CGATTCAGAAAAAT 1 promoter_21 ( 94) ATTTCCGGTAACCT 1 promoter_49 ( 78) TCTTTCAAAAAACG 1 promoter_46 ( 55) TTATGCAGAAAAGC 1 promoter_44 ( 104) TCATGCTGACAGAA 1 promoter_16 ( 14) CCTTTCAGCGTGGT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif KYTTBCVGAARGVT MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 14 n= 6850 bayes= 8.01385 E= 1.3e-003 -318 6 46 64 -1164 142 -39 -10 -60 -1164 -1164 143 -1164 -1164 -1164 173 -1164 57 87 6 -1164 225 -1164 -1164 -1 6 110 -227 -160 -1164 215 -1164 114 6 -1164 -94 140 -43 -113 -1164 99 -275 87 -326 -60 6 120 -127 14 42 87 -326 -86 -175 -39 105 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif KYTTBCVGAARGVT MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 14 nsites= 32 E= 1.3e-003 0.031250 0.218750 0.281250 0.468750 0.000000 0.562500 0.156250 0.281250 0.187500 0.000000 0.000000 0.812500 0.000000 0.000000 0.000000 1.000000 0.000000 0.312500 0.375000 0.312500 0.000000 1.000000 0.000000 0.000000 0.281250 0.218750 0.437500 0.062500 0.093750 0.000000 0.906250 0.000000 0.625000 0.218750 0.000000 0.156250 0.750000 0.156250 0.093750 0.000000 0.562500 0.031250 0.375000 0.031250 0.187500 0.218750 0.468750 0.125000 0.312500 0.281250 0.375000 0.031250 0.156250 0.062500 0.156250 0.625000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif KYTTBCVGAARGVT MEME-1 regular expression -------------------------------------------------------------------------------- [TGC][CT]TT[GCT]C[GAC]G[AC]A[AG][GC][GAC]T -------------------------------------------------------------------------------- Time 2.35 secs. ******************************************************************************** ******************************************************************************** MOTIF RRAAAAAACCK MEME-2 width = 11 sites = 27 llr = 219 E-value = 1.1e+000 ******************************************************************************** -------------------------------------------------------------------------------- Motif RRAAAAAACCK MEME-2 Description -------------------------------------------------------------------------------- Simplified A 3687a866::: pos.-specific C 1:23::1297: probability G 54::::12:36 matrix T 1::::22:1:3 bits 2.3 2.1 1.8 * * 1.6 * * Relative 1.4 * ** Entropy 1.1 ***** ** (11.7 bits) 0.9 ***** *** 0.7 ***** **** 0.5 ****** **** 0.2 *********** 0.0 ----------- Multilevel GAAAAAAACCG consensus AG C TTG GT sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RRAAAAAACCK MEME-2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ----------- promoter_8 6 2.76e-07 TTACC GAAAAAAACCG GTCAGCCCCC promoter_30 134 3.34e-06 TCAGCGAACA GGAAAAACCCG GACATC promoter_41 70 4.33e-06 AGAAGAGAAA CAAAAAAACCG AACTTGCAAA promoter_6 140 4.33e-06 ATTATTACAC GGAAAAAACCT promoter_47 130 7.75e-06 CAATGAAAGC AAAAAAACCCG GACAAAAACA promoter_34 15 1.37e-05 GACCAGAAGC GAAAAATCCCG TTCGAGAAAT promoter_28 30 1.37e-05 GGCTCGTTCA GGAAAAAGCCT GTAAACAGGG promoter_18 35 1.37e-05 GGCGGGGTCT GAAAAAAACGT TTTTTGCTAT promoter_21 130 1.59e-05 CCTTTGCGTT GACAAAAACGG AATATGTACC promoter_11 138 1.59e-05 TACAGCAACA AGAAAAAACCT CT promoter_25 50 1.92e-05 TCAACTGCGT GAAAAATACCT GTGCGACATC promoter_27 137 3.04e-05 CCCATATAAA GAACAAAGCCT GTT promoter_15 64 3.41e-05 TTGTACCTTC AAAAAACACCG ACTTTTTTTA promoter_42 76 7.74e-05 CGTTTGGGAT GACCATAACCG GCTTTTAAGC promoter_24 13 1.19e-04 TAAAAGATAT AAAAAAAATCG AATTCAAGTC promoter_13 75 1.40e-04 GCAGGAAGAA CAAAAACACGG CGTCTAAAGC promoter_14 8 1.67e-04 GGCAGTC CGACAATCCCG CAGCGGAGAG promoter_50 68 2.25e-04 TATCGAATTA AAAAATGACCT TAAGGATAAA promoter_29 43 2.25e-04 GCTTTATGGA AGACAATGCCT GTAAAAACCT promoter_26 63 2.25e-04 ACTCAATAGA TACAAATACCG TGTAAACAAT promoter_10 36 2.25e-04 TCCTTGTCGT TAAAATAACGG ACTTCCTTGC promoter_4 3 2.25e-04 TC GGACATGACGG GTTTTTACGA promoter_23 130 2.39e-04 TTCTGAACAC AGACATAGCGG AACGCTCTAT promoter_32 2 2.71e-04 G GGAAAAGACCA GCTTTGTTGT promoter_7 2 2.89e-04 C GGCCAATGCCT TACCTTTAAG promoter_44 25 3.69e-04 AAACAATAAC AAAAAAAGTGG AAAAACAGAT promoter_48 131 4.12e-04 TAAAGAAAAA CACAATACCGG GCTTCCCGA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RRAAAAAACCK MEME-2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- promoter_8 2.8e-07 5_[+2]_134 promoter_30 3.3e-06 133_[+2]_6 promoter_41 4.3e-06 69_[+2]_70 promoter_6 4.3e-06 139_[+2] promoter_47 7.7e-06 129_[+2]_10 promoter_34 1.4e-05 14_[+2]_125 promoter_28 1.4e-05 29_[+2]_110 promoter_18 1.4e-05 34_[+2]_105 promoter_21 1.6e-05 129_[+2]_10 promoter_11 1.6e-05 137_[+2]_2 promoter_25 1.9e-05 49_[+2]_90 promoter_27 3e-05 136_[+2]_3 promoter_15 3.4e-05 63_[+2]_76 promoter_42 7.7e-05 75_[+2]_64 promoter_24 0.00012 12_[+2]_127 promoter_13 0.00014 74_[+2]_65 promoter_14 0.00017 7_[+2]_132 promoter_50 0.00023 67_[+2]_72 promoter_29 0.00023 42_[+2]_97 promoter_26 0.00023 62_[+2]_77 promoter_10 0.00023 35_[+2]_104 promoter_4 0.00023 2_[+2]_137 promoter_23 0.00024 129_[+2]_10 promoter_32 0.00027 1_[+2]_138 promoter_7 0.00029 1_[+2]_138 promoter_44 0.00037 24_[+2]_115 promoter_48 0.00041 130_[+2]_9 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RRAAAAAACCK MEME-2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF RRAAAAAACCK width=11 seqs=27 promoter_8 ( 6) GAAAAAAACCG 1 promoter_30 ( 134) GGAAAAACCCG 1 promoter_41 ( 70) CAAAAAAACCG 1 promoter_6 ( 140) GGAAAAAACCT 1 promoter_47 ( 130) AAAAAAACCCG 1 promoter_34 ( 15) GAAAAATCCCG 1 promoter_28 ( 30) GGAAAAAGCCT 1 promoter_18 ( 35) GAAAAAAACGT 1 promoter_21 ( 130) GACAAAAACGG 1 promoter_11 ( 138) AGAAAAAACCT 1 promoter_25 ( 50) GAAAAATACCT 1 promoter_27 ( 137) GAACAAAGCCT 1 promoter_15 ( 64) AAAAAACACCG 1 promoter_42 ( 76) GACCATAACCG 1 promoter_24 ( 13) AAAAAAAATCG 1 promoter_13 ( 75) CAAAAACACGG 1 promoter_14 ( 8) CGACAATCCCG 1 promoter_50 ( 68) AAAAATGACCT 1 promoter_29 ( 43) AGACAATGCCT 1 promoter_26 ( 63) TACAAATACCG 1 promoter_10 ( 36) TAAAATAACGG 1 promoter_4 ( 3) GGACATGACGG 1 promoter_23 ( 130) AGACATAGCGG 1 promoter_32 ( 2) GGAAAAGACCA 1 promoter_7 ( 2) GGCCAATGCCT 1 promoter_44 ( 25) AAAAAAAGTGG 1 promoter_48 ( 131) CACAATACCGG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RRAAAAAACCK MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 11 n= 7000 bayes= 8.10114 E= 1.1e+000 6 -51 123 -202 115 -1140 86 -1140 152 -18 -1140 -1140 138 30 -1140 -1140 182 -1140 -1140 -1140 145 -1140 -1140 -44 106 -151 -88 -44 106 -18 12 -1140 -1140 214 -1140 -202 -1140 174 53 -1140 -294 -1140 162 15 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RRAAAAAACCK MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 11 nsites= 27 E= 1.1e+000 0.296296 0.148148 0.481481 0.074074 0.629630 0.000000 0.370370 0.000000 0.814815 0.185185 0.000000 0.000000 0.740741 0.259259 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.777778 0.000000 0.000000 0.222222 0.592593 0.074074 0.111111 0.222222 0.592593 0.185185 0.222222 0.000000 0.000000 0.925926 0.000000 0.074074 0.000000 0.703704 0.296296 0.000000 0.037037 0.000000 0.629630 0.333333 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RRAAAAAACCK MEME-2 regular expression -------------------------------------------------------------------------------- [GA][AG]A[AC]A[AT][AT][AG]C[CG][GT] -------------------------------------------------------------------------------- Time 4.49 secs. ******************************************************************************** ******************************************************************************** MOTIF YTTTTTTTDWWCWTT MEME-3 width = 15 sites = 27 llr = 224 E-value = 2.4e+005 ******************************************************************************** -------------------------------------------------------------------------------- Motif YTTTTTTTDWWCWTT MEME-3 Description -------------------------------------------------------------------------------- Simplified A :132:3:234334:: pos.-specific C 6:::::1::12611: probability G 1:::1:::4:1::2: matrix T 39789798344247a bits 2.3 2.1 1.8 1.6 * Relative 1.4 * * * Entropy 1.1 * ** ** * (12.0 bits) 0.9 * ***** * 0.7 ** ***** * * 0.5 ******** * **** 0.2 ********** **** 0.0 --------------- Multilevel CTTTTTTTGATCATT consensus T A A ATAAT sequence T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif YTTTTTTTDWWCWTT MEME-3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------- promoter_34 122 7.87e-08 CGATCGGTTG CTTTTTTTGTACTTT CCTGATTATC promoter_9 54 2.39e-07 TGAATCCTGC TTTTTTTTGATCTTT CTCCGCTTTG promoter_45 58 3.93e-07 CTCGGTGTAA CTTTTTTTATGCTTT GAACGCTCCG promoter_36 99 2.31e-06 TTAAAGCTAA CTATTTTTAAGCTTT ATCTTGAAAA promoter_15 48 4.75e-06 GTGTCAATCT GTTTTTTTGTACCTT CAAAAAACAC promoter_31 89 5.36e-06 AGGAAATCAT CTTTTTTTGCCATTT TCCCTGCTGT promoter_43 112 9.14e-06 CGGTCCAGAG CTTTTTTTGTTTTCT TCAAATGCAG promoter_47 34 1.17e-05 CTTTTATGCT CTTTTATTTCACTTT TTCAACATTT promoter_1 126 2.09e-05 CTTCCCCTCG TTTTTTTTACTAATT CTATGCCTGT promoter_46 116 2.29e-05 ATTTGCTTTC CTGTTTTTGACCCTT TGTTTCGCTT promoter_25 110 3.18e-05 TTATAATTTA CATTTATTGATAATT CATTCGCTCC promoter_33 74 3.52e-05 TAAAAAGATG CTTTTTTAGTGAAGT CATACGGCTG promoter_10 84 4.23e-05 AATAAATTGT TTCTTTTTTTTCTTT GGATTTTTAA promoter_6 121 7.39e-05 CTTAAGCGGG TTATTATTAATTATT ACACGGAAAA promoter_3 96 8.83e-05 CTAATTCGGG CTAATTTTGTTATCT TGAGGTTTAT promoter_38 38 9.57e-05 GAACGCCCGG GTTTTATAAATCAGT AAAAATTCAT promoter_32 128 1.04e-04 GTTTCTTTCC CTTTTACTAACTTTT GTTCAGGT promoter_23 39 1.31e-04 AGCTGTTTAT CATATTTTTATTATT ATACTAAAAG promoter_14 121 1.31e-04 AAAAGCAAAT TTATTTTATAAAATT ACAGGCTAAG promoter_12 1 1.42e-04 . CTTTTATTCTCCCGT CTTTAATTCC promoter_4 91 1.53e-04 TTCTTATATT CTTTGTTTTATCTAT TGAAACGGGA promoter_40 37 1.64e-04 ACTTTTCAGC CTTTTTCATTATATT CGAAGTCCTG promoter_2 105 1.90e-04 CTGTAATAAA TTTATTTTAACAACT ATGTTTCACG promoter_18 80 2.67e-04 TATTTTATCG TTTTGTCTGTGCCTT TGCTGTGGAT promoter_37 130 2.85e-04 GGATGGATGT GTAATTTAAATCAGT CATGCG promoter_13 44 3.65e-04 TCGGAAGGCT TTATTTTTTTACAGG AAAGATGCAG promoter_19 89 6.33e-04 AGAATTAAAT GAAATATTTTACATT GATAAACTTT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif YTTTTTTTDWWCWTT MEME-3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- promoter_34 7.9e-08 121_[+3]_14 promoter_9 2.4e-07 53_[+3]_82 promoter_45 3.9e-07 57_[+3]_78 promoter_36 2.3e-06 98_[+3]_37 promoter_15 4.7e-06 47_[+3]_88 promoter_31 5.4e-06 88_[+3]_47 promoter_43 9.1e-06 111_[+3]_24 promoter_47 1.2e-05 33_[+3]_102 promoter_1 2.1e-05 125_[+3]_10 promoter_46 2.3e-05 115_[+3]_20 promoter_25 3.2e-05 109_[+3]_26 promoter_33 3.5e-05 73_[+3]_62 promoter_10 4.2e-05 83_[+3]_52 promoter_6 7.4e-05 120_[+3]_15 promoter_3 8.8e-05 95_[+3]_40 promoter_38 9.6e-05 37_[+3]_98 promoter_32 0.0001 127_[+3]_8 promoter_23 0.00013 38_[+3]_97 promoter_14 0.00013 120_[+3]_15 promoter_12 0.00014 [+3]_135 promoter_4 0.00015 90_[+3]_45 promoter_40 0.00016 36_[+3]_99 promoter_2 0.00019 104_[+3]_31 promoter_18 0.00027 79_[+3]_56 promoter_37 0.00029 129_[+3]_6 promoter_13 0.00036 43_[+3]_92 promoter_19 0.00063 88_[+3]_47 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif YTTTTTTTDWWCWTT MEME-3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF YTTTTTTTDWWCWTT width=15 seqs=27 promoter_34 ( 122) CTTTTTTTGTACTTT 1 promoter_9 ( 54) TTTTTTTTGATCTTT 1 promoter_45 ( 58) CTTTTTTTATGCTTT 1 promoter_36 ( 99) CTATTTTTAAGCTTT 1 promoter_15 ( 48) GTTTTTTTGTACCTT 1 promoter_31 ( 89) CTTTTTTTGCCATTT 1 promoter_43 ( 112) CTTTTTTTGTTTTCT 1 promoter_47 ( 34) CTTTTATTTCACTTT 1 promoter_1 ( 126) TTTTTTTTACTAATT 1 promoter_46 ( 116) CTGTTTTTGACCCTT 1 promoter_25 ( 110) CATTTATTGATAATT 1 promoter_33 ( 74) CTTTTTTAGTGAAGT 1 promoter_10 ( 84) TTCTTTTTTTTCTTT 1 promoter_6 ( 121) TTATTATTAATTATT 1 promoter_3 ( 96) CTAATTTTGTTATCT 1 promoter_38 ( 38) GTTTTATAAATCAGT 1 promoter_32 ( 128) CTTTTACTAACTTTT 1 promoter_23 ( 39) CATATTTTTATTATT 1 promoter_14 ( 121) TTATTTTATAAAATT 1 promoter_12 ( 1) CTTTTATTCTCCCGT 1 promoter_4 ( 91) CTTTGTTTTATCTAT 1 promoter_40 ( 37) CTTTTTCATTATATT 1 promoter_2 ( 105) TTTATTTTAACAACT 1 promoter_18 ( 80) TTTTGTCTGTGCCTT 1 promoter_37 ( 130) GTAATTTAAATCAGT 1 promoter_13 ( 44) TTATTTTTTTACAGG 1 promoter_19 ( 89) GAAATATTTTACATT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif YTTTTTTTDWWCWTT MEME-3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 6800 bayes= 8.05916 E= 2.4e+005 -1140 140 -47 -2 -135 -1140 -1140 156 -13 -250 -246 115 -62 -1140 -1140 144 -1140 -1140 -147 162 -13 -1140 -1140 130 -1140 -92 -1140 156 -62 -1140 -1140 144 6 -250 86 -2 65 -92 -1140 56 -13 -18 -47 44 -13 140 -1140 -70 65 -51 -1140 44 -294 -92 -14 115 -1140 -1140 -246 168 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif YTTTTTTTDWWCWTT MEME-3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 27 E= 2.4e+005 0.000000 0.555556 0.148148 0.296296 0.111111 0.000000 0.000000 0.888889 0.259259 0.037037 0.037037 0.666667 0.185185 0.000000 0.000000 0.814815 0.000000 0.000000 0.074074 0.925926 0.259259 0.000000 0.000000 0.740741 0.000000 0.111111 0.000000 0.888889 0.185185 0.000000 0.000000 0.814815 0.296296 0.037037 0.370370 0.296296 0.444444 0.111111 0.000000 0.444444 0.259259 0.185185 0.148148 0.407407 0.259259 0.555556 0.000000 0.185185 0.444444 0.148148 0.000000 0.407407 0.037037 0.111111 0.185185 0.666667 0.000000 0.000000 0.037037 0.962963 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif YTTTTTTTDWWCWTT MEME-3 regular expression -------------------------------------------------------------------------------- [CT]T[TA]TT[TA]TT[GAT][AT][TA][CA][AT]TT -------------------------------------------------------------------------------- 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 ------------- ---------------- ------------- promoter_1 5.57e-02 125_[+3(2.09e-05)]_10 promoter_2 8.60e-03 40_[+1(7.90e-05)]_96 promoter_3 5.09e-02 95_[+3(8.83e-05)]_40 promoter_4 7.87e-03 150 promoter_5 7.81e-03 28_[+1(7.90e-05)]_108 promoter_6 3.46e-04 120_[+3(7.39e-05)]_4_[+2(4.33e-06)] promoter_7 1.94e-02 150 promoter_8 9.80e-06 5_[+2(2.76e-07)]_62_[+1(1.20e-05)]_\ 58 promoter_9 5.13e-04 53_[+3(2.39e-07)]_39_[+3(4.68e-05)]_\ 28 promoter_10 7.22e-05 50_[+1(2.52e-05)]_19_[+3(4.23e-05)]_\ 52 promoter_11 5.21e-05 29_[+1(1.51e-06)]_94_[+2(1.59e-05)]_\ 2 promoter_12 1.91e-01 150 promoter_13 3.10e-05 29_[+1(1.81e-06)]_107 promoter_14 6.13e-04 150 promoter_15 2.99e-06 27_[+1(3.97e-05)]_6_[+3(4.75e-06)]_\ 1_[+2(3.41e-05)]_76 promoter_16 6.65e-02 150 promoter_17 2.99e-02 76_[+1(3.18e-05)]_60 promoter_18 1.68e-03 34_[+2(1.37e-05)]_105 promoter_19 2.65e-03 114_[+1(7.90e-06)]_22 promoter_20 7.06e-02 150 promoter_21 4.43e-03 129_[+2(1.59e-05)]_10 promoter_22 4.24e-01 150 promoter_23 1.21e-03 150 promoter_24 8.16e-05 89_[+1(5.62e-07)]_47 promoter_25 2.44e-05 49_[+2(1.92e-05)]_49_[+3(3.18e-05)]_\ 26 promoter_26 3.55e-05 15_[+1(7.19e-08)]_121 promoter_27 4.54e-03 136_[+2(3.04e-05)]_3 promoter_28 4.59e-06 29_[+2(1.37e-05)]_90_[+1(1.58e-07)]_\ 6 promoter_29 2.04e-02 150 promoter_30 2.97e-03 133_[+2(3.34e-06)]_6 promoter_31 2.12e-04 88_[+3(5.36e-06)]_47 promoter_32 1.45e-02 150 promoter_33 1.42e-03 73_[+3(3.52e-05)]_62 promoter_34 6.48e-08 14_[+2(1.37e-05)]_60_[+1(8.65e-05)]_\ 22_[+3(7.87e-08)]_14 promoter_35 2.76e-02 134_[+1(8.65e-05)]_2 promoter_36 2.47e-03 98_[+3(2.31e-06)]_37 promoter_37 1.57e-02 150 promoter_38 1.02e-01 37_[+3(9.57e-05)]_98 promoter_39 1.04e-04 33_[+1(7.19e-08)]_103 promoter_40 9.05e-02 150 promoter_41 9.05e-05 69_[+2(4.33e-06)]_12_[+1(3.97e-05)]_\ 44 promoter_42 5.64e-05 49_[+1(2.24e-05)]_12_[+2(7.74e-05)]_\ 64 promoter_43 4.87e-04 33_[+1(4.89e-05)]_64_[+3(9.14e-06)]_\ 24 promoter_44 6.33e-02 150 promoter_45 2.56e-04 57_[+3(3.93e-07)]_78 promoter_46 2.57e-03 115_[+3(2.29e-05)]_20 promoter_47 2.94e-05 33_[+3(1.17e-05)]_81_[+2(7.75e-06)]_\ 10 promoter_48 2.33e-01 150 promoter_49 2.34e-02 150 promoter_50 2.68e-03 16_[+1(1.05e-05)]_60_[+1(2.84e-05)]_\ 46 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (3) found. ******************************************************************************** CPU: noble-meme.grid.gs.washington.edu ********************************************************************************