******************************************************************************** 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= house_keeping_promoters.txt CONTROL SEQUENCES= --none-- ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 1 1.0000 100 2 1.0000 100 3 1.0000 100 4 1.0000 100 5 1.0000 100 6 1.0000 100 7 1.0000 100 8 1.0000 100 9 1.0000 100 10 1.0000 100 11 1.0000 100 12 1.0000 100 13 1.0000 100 14 1.0000 100 15 1.0000 100 16 1.0000 100 17 1.0000 100 18 1.0000 100 19 1.0000 100 20 1.0000 100 21 1.0000 100 22 1.0000 100 23 1.0000 100 24 1.0000 100 25 1.0000 100 26 1.0000 100 27 1.0000 100 28 1.0000 100 29 1.0000 100 30 1.0000 100 31 1.0000 100 32 1.0000 100 33 1.0000 100 34 1.0000 100 35 1.0000 100 36 1.0000 100 37 1.0000 100 38 1.0000 100 39 1.0000 100 40 1.0000 100 41 1.0000 100 42 1.0000 100 43 1.0000 100 44 1.0000 100 45 1.0000 100 46 1.0000 100 47 1.0000 100 48 1.0000 100 49 1.0000 100 50 1.0000 100 51 1.0000 100 52 1.0000 100 53 1.0000 100 54 1.0000 100 55 1.0000 100 56 1.0000 100 57 1.0000 100 58 1.0000 100 59 1.0000 100 60 1.0000 100 61 1.0000 100 62 1.0000 100 63 1.0000 100 64 1.0000 100 65 1.0000 100 66 1.0000 100 67 1.0000 100 68 1.0000 100 69 1.0000 100 70 1.0000 100 71 1.0000 100 72 1.0000 100 73 1.0000 100 74 1.0000 100 75 1.0000 100 76 1.0000 100 77 1.0000 100 78 1.0000 100 79 1.0000 100 80 1.0000 100 81 1.0000 100 82 1.0000 100 83 1.0000 100 84 1.0000 100 85 1.0000 100 86 1.0000 100 87 1.0000 100 88 1.0000 100 89 1.0000 100 90 1.0000 100 91 1.0000 100 92 1.0000 100 93 1.0000 100 94 1.0000 100 95 1.0000 100 96 1.0000 100 97 1.0000 100 98 1.0000 100 99 1.0000 100 100 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 house_keeping_promoters.txt -dna -mod zoops -nmotifs 3 -minw 6 -maxw 50 model: mod= zoops nmotifs= 3 evt= inf objective function: em= E-value of product of p-values starts= E-value of product of p-values strands: + width: minw= 6 maxw= 50 nsites: minsites= 2 maxsites= 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= 10000 N= 100 sample: seed= 0 hsfrac= 0 searchsize= 10000 norand= no csites= 1000 Letter frequencies in dataset: A 0.347 C 0.14 G 0.194 T 0.32 Background letter frequencies (from file dataset with add-one prior applied): A 0.347 C 0.14 G 0.194 T 0.32 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF AGGAGG MEME-1 width = 6 sites = 45 llr = 337 E-value = 1.9e-016 ******************************************************************************** -------------------------------------------------------------------------------- Motif AGGAGG MEME-1 Description -------------------------------------------------------------------------------- Simplified A 7::8:: pos.-specific C 1::::: probability G 1aa2aa matrix T 1::::: bits 2.8 2.6 2.3 ** ** 2.0 ** ** Relative 1.7 ** ** Entropy 1.4 ** ** (10.8 bits) 1.1 ***** 0.9 ***** 0.6 ***** 0.3 ****** 0.0 ------ Multilevel AGGAGG consensus sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AGGAGG MEME-1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------ 100 90 1.71e-04 GATAACAAAA AGGAGG ACGAC 96 46 1.71e-04 CTCTCTGAGA AGGAGG CTTTTTTACG 92 85 1.71e-04 GTACCTAGTT AGGAGG GGAACTGAAC 91 87 1.71e-04 GCCAAAAATG AGGAGG ATCATAGA 81 86 1.71e-04 CGACTTAAAA AGGAGG ATGATTCAA 68 88 1.71e-04 TTTAATAATC AGGAGG ATGAATC 66 88 1.71e-04 AACGTTATCA AGGAGG TCGTCAT 65 87 1.71e-04 CCTAAATAGA AGGAGG CGCACAAA 60 85 1.71e-04 CATTTGTTTC AGGAGG TGATCATTTT 53 90 1.71e-04 GCAGTTTTAT AGGAGG AAAAA 52 89 1.71e-04 TATGAATGTA AGGAGG AAAATC 50 88 1.71e-04 TGATTTGGGA AGGAGG AGCTCAT 47 85 1.71e-04 TACTTAAAAA AGGAGG TTTGATTACA 34 87 1.71e-04 AAGATTGGCT AGGAGG TCTTTTTT 33 89 1.71e-04 TTGCTTTGGC AGGAGG GATTCT 28 86 1.71e-04 AGGTATGATA AGGAGG CGCTTTCTT 19 87 1.71e-04 CACAAATAAC AGGAGG TTATGTTG 14 85 1.71e-04 ATTAGCTGAG AGGAGG CCGGTTTTCC 13 88 1.71e-04 GTAGGCGAAA AGGAGG GAAAATA 10 88 1.71e-04 AAGTCAGTAA AGGAGG GGGTTGA 6 89 1.71e-04 GGAAACAGAG AGGAGG GGCCAT 2 87 1.71e-04 TGAATAACGG AGGAGG GCAAACCC 1 82 1.71e-04 TTCTAAGAAA AGGAGG GACGTGCCGG 70 86 2.66e-04 TCGATTTAAA GGGAGG CTATGTGAC 55 43 2.66e-04 TTTATGCGCT GGGAGG TTGTTCAAAA 38 86 2.66e-04 GTTTTTTATT GGGAGG TAAGCGAAT 25 86 2.66e-04 TAAAGATTAG GGGAGG TATGACAAT 22 87 2.66e-04 CGATTTTATA GGGAGG ACTGTCAG 18 34 2.66e-04 CTTTCATATT GGGAGG GCAAATGGTA 84 87 3.61e-04 TTATTTTCAG AGGGGG AATGATTT 82 93 3.61e-04 TGTGTAAAAA AGGGGG GC 63 88 3.61e-04 GAAACGGCGA AGGGGG ATTTACC 57 87 3.61e-04 TTTTAATAAC AGGGGG GATAGCAG 27 88 3.61e-04 GGTACAAAAC AGGGGG AGAAGGC 24 86 3.61e-04 AAGGTTACTA AGGGGG GGGATTCTA 15 88 3.61e-04 ATTTTAAAAC AGGGGG CATCCTC 67 90 4.30e-04 CAGCCAGACA CGGAGG ATAGC 64 88 4.30e-04 AAAACGGATA CGGAGG GGTTGGC 29 87 4.30e-04 CGCATAACGA CGGAGG AGATTTAC 79 88 5.87e-04 AGAAAAAGGA TGGAGG CCATAAT 44 87 5.87e-04 ATACCATATA TGGAGG TGGATGAT 40 85 5.87e-04 ACGACAAAAT TGGAGG CTTTGGTTAC 37 85 5.87e-04 GTAAGTTTGG TGGAGG TGTATGTTTT 23 90 5.87e-04 GTTCAACCTA TGGAGG CTGAA 5 88 5.87e-04 AAAGGGATAT TGGAGG CCAATAA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AGGAGG MEME-1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 100 0.00017 89_[+1]_5 96 0.00017 45_[+1]_49 92 0.00017 84_[+1]_10 91 0.00017 86_[+1]_8 81 0.00017 85_[+1]_9 68 0.00017 87_[+1]_7 66 0.00017 87_[+1]_7 65 0.00017 86_[+1]_8 60 0.00017 84_[+1]_10 53 0.00017 89_[+1]_5 52 0.00017 88_[+1]_6 50 0.00017 87_[+1]_7 47 0.00017 84_[+1]_10 34 0.00017 86_[+1]_8 33 0.00017 88_[+1]_6 28 0.00017 85_[+1]_9 19 0.00017 86_[+1]_8 14 0.00017 84_[+1]_10 13 0.00017 87_[+1]_7 10 0.00017 87_[+1]_7 6 0.00017 88_[+1]_6 2 0.00017 86_[+1]_8 1 0.00017 81_[+1]_13 70 0.00027 85_[+1]_9 55 0.00027 42_[+1]_52 38 0.00027 85_[+1]_9 25 0.00027 85_[+1]_9 22 0.00027 86_[+1]_8 18 0.00027 33_[+1]_61 84 0.00036 86_[+1]_8 82 0.00036 92_[+1]_2 63 0.00036 87_[+1]_7 57 0.00036 86_[+1]_8 27 0.00036 87_[+1]_7 24 0.00036 85_[+1]_9 15 0.00036 87_[+1]_7 67 0.00043 89_[+1]_5 64 0.00043 87_[+1]_7 29 0.00043 86_[+1]_8 79 0.00059 87_[+1]_7 44 0.00059 86_[+1]_8 40 0.00059 84_[+1]_10 37 0.00059 84_[+1]_10 23 0.00059 89_[+1]_5 5 0.00059 87_[+1]_7 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AGGAGG MEME-1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF AGGAGG width=6 seqs=45 100 ( 90) AGGAGG 1 96 ( 46) AGGAGG 1 92 ( 85) AGGAGG 1 91 ( 87) AGGAGG 1 81 ( 86) AGGAGG 1 68 ( 88) AGGAGG 1 66 ( 88) AGGAGG 1 65 ( 87) AGGAGG 1 60 ( 85) AGGAGG 1 53 ( 90) AGGAGG 1 52 ( 89) AGGAGG 1 50 ( 88) AGGAGG 1 47 ( 85) AGGAGG 1 34 ( 87) AGGAGG 1 33 ( 89) AGGAGG 1 28 ( 86) AGGAGG 1 19 ( 87) AGGAGG 1 14 ( 85) AGGAGG 1 13 ( 88) AGGAGG 1 10 ( 88) AGGAGG 1 6 ( 89) AGGAGG 1 2 ( 87) AGGAGG 1 1 ( 82) AGGAGG 1 70 ( 86) GGGAGG 1 55 ( 43) GGGAGG 1 38 ( 86) GGGAGG 1 25 ( 86) GGGAGG 1 22 ( 87) GGGAGG 1 18 ( 34) GGGAGG 1 84 ( 87) AGGGGG 1 82 ( 93) AGGGGG 1 63 ( 88) AGGGGG 1 57 ( 87) AGGGGG 1 27 ( 88) AGGGGG 1 24 ( 86) AGGGGG 1 15 ( 88) AGGGGG 1 67 ( 90) CGGAGG 1 64 ( 88) CGGAGG 1 29 ( 87) CGGAGG 1 79 ( 88) TGGAGG 1 44 ( 87) TGGAGG 1 40 ( 85) TGGAGG 1 37 ( 85) TGGAGG 1 23 ( 90) TGGAGG 1 5 ( 88) TGGAGG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AGGAGG MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 6 n= 9500 bayes= 8.76414 E= 1.9e-016 94 -107 -54 -126 -1214 -1214 236 -1214 -1214 -1214 236 -1214 128 -1214 -32 -1214 -1214 -1214 236 -1214 -1214 -1214 236 -1214 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AGGAGG MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 6 nsites= 45 E= 1.9e-016 0.666667 0.066667 0.133333 0.133333 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.844444 0.000000 0.155556 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AGGAGG MEME-1 regular expression -------------------------------------------------------------------------------- AGGAGG -------------------------------------------------------------------------------- Time 5.89 secs. ******************************************************************************** ******************************************************************************** MOTIF BCTYYTTTYTTKTNW MEME-2 width = 15 sites = 45 llr = 367 E-value = 3.2e-008 ******************************************************************************** -------------------------------------------------------------------------------- Motif BCTYYTTTYTTKTNW MEME-2 Description -------------------------------------------------------------------------------- Simplified A 1::1:1::23::123 pos.-specific C 472461:2421::21 probability G 2::1:::1::14:4: matrix T 337447a74686926 bits 2.8 2.6 2.3 2.0 Relative 1.7 * * Entropy 1.4 * * * (11.8 bits) 1.1 * * * * * 0.9 ** * * * * 0.6 ******** *** 0.3 *************** 0.0 --------------- Multilevel CCTTCTTTCTTTTGT consensus TTCCT CTA G AA sequence G C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif BCTYYTTTYTTKTNW MEME-2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------- 12 10 8.76e-08 ATTAGAAAC CCTTTTTTCTTTTGT CTTGTAAAAG 21 36 8.24e-07 GAATTGAATT CCTCCTTCCTCTTAT GACTTCCTGC 1 33 1.55e-06 AGCGCCATTT GCTCTTTTTTTGTGT TCTATAACAG 39 19 1.84e-06 TGGACATCCG GCTTCTTTTTTTTGC GGTTGACTAT 74 1 2.16e-06 . CCCCTATCCTTTTCT GTTATTATAG 72 38 2.16e-06 CTTTGACAAA TCTTCTTTCATTTAT TAATATTTTA 75 1 3.52e-06 . CCCCTTTCCTTTCGT TACAATGATC 92 33 4.73e-06 TGTAATGAGA GCTTTTTTCTTTTTT AAAGGGAATT 67 3 4.73e-06 TC CCTTCCTCCCTTTTC TATAATAAGG 96 29 8.06e-06 AGATGTTAAG CCTCCTTCTCTCTGA GAAGGAGGCT 28 1 8.06e-06 . TCTGCTTTCATTTCA ATCATACTCC 68 3 9.38e-06 CT TCTCCTTTATTTTAC AAGAAAAAGA 98 41 1.07e-05 ATCGGAAGTA CCCACTTTTTTGTGA TATAGTAACT 40 29 1.39e-05 GCGCCAGCTG TCTTTTTTTATGTGT TTTTTTCGGT 27 18 1.39e-05 GCGCCGGTCG CTCCCTTTATTGTAT GGCCGCGGTC 49 30 1.56e-05 TAAATGGATT TCTGTTTTCTTTTTT TATTCAATTT 47 4 1.56e-05 GCG GCCCCTTTCACTTCA GATCGTGAAT 53 67 2.22e-05 ATAGAGCACT CCTATTTTTTTGTGC AGTTTTATAG 52 16 2.22e-05 GTCCAACGTT TTTTCCTCCTTGTCA CGCTTACATT 60 39 2.51e-05 TGTTTTTTTA GCTTTTTTCTTGACT GTTCAGTCTG 63 13 4.86e-05 ATGCTGCTCG TCTTTTTTATTGTTT TTTAAAACTT 81 23 5.37e-05 TTAAAGTGTA CCTCCATTTCCTTAT AATAAAAAGG 73 32 5.96e-05 ATGTTTTTTA ATTCCTTTTTTTTCA TTTTTCAATC 94 45 6.64e-05 CAAGCGTCAG GTTTTTTCTCTTTGT TTTTTATATA 88 2 8.12e-05 A TCCCCCTCAATTTTT TCATCTTTCT 65 52 8.12e-05 AGACTGGCAC ACTTCTTGCATTTAT AATGGTGAAC 7 33 9.79e-05 GTATAATAAC CTCGTTTTTATTTGT GCCGCGGTAA 91 64 1.07e-04 TGATTGGTGT CCGTTTTTTATTTGC CAAAAATGAG 35 32 1.41e-04 GCTTAACAGC CCATCCTTTTTGTAT TGAAAAAAAC 6 60 1.41e-04 CTAGACCAAA GCGTTTTTCTGTTCT CGCAGGAAAC 99 2 1.68e-04 T TCTCCTTTCAGCTAA AAACACAAAA 84 71 1.68e-04 CGGGAAAGTG GTTTTTTTATTTTCA GAGGGGGAAT 32 33 1.68e-04 TTTTTTATCA TCCACTTACTTGTCT CCGTCTCTAA 87 1 1.84e-04 . TCTCTATGATTTTGT TTTATAATGT 69 37 1.99e-04 TTTCTGCTCA CTTTCTTTCAGGAGT GAAAATCGAG 70 30 2.34e-04 AAGCGGTATG CTTGCTTTTTTGAAT GGTGAATGAT 43 75 2.34e-04 ATTTTGTAAA ACTTTTTCACTGTGA AAGGAGTTAC 38 17 2.53e-04 AATAGAGCAA CTTTTTTTGTTTTCA AAAAACATAA 31 2 3.21e-04 A TCCCCCTGTCGGTAT TTTCTTATCA 95 59 3.47e-04 TATGTAAGGG TTTTCATTATTTTTT TATAAAAATC 76 32 3.47e-04 GTATAAAAAA GCCGTTTGCATGTAA TGTGCAACTT 61 51 3.47e-04 GCGTTATGGT TTTCCCTCCTTTATA ATCGTGTCAC 58 61 4.95e-04 ATCAAAGGAA TTTTCATTCATTCGC CTAAATATGT 83 14 6.11e-04 AGTATGAGAA ATTCCATTTTTGTTA AAAGGAAAAA 22 3 6.11e-04 CT CTTACTTTTCTATGT AAGTTCTGAT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif BCTYYTTTYTTKTNW MEME-2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 12 8.8e-08 9_[+2]_76 21 8.2e-07 35_[+2]_50 1 1.5e-06 32_[+2]_53 39 1.8e-06 18_[+2]_67 74 2.2e-06 [+2]_85 72 2.2e-06 37_[+2]_48 75 3.5e-06 [+2]_85 92 4.7e-06 32_[+2]_53 67 4.7e-06 2_[+2]_83 96 8.1e-06 28_[+2]_57 28 8.1e-06 [+2]_85 68 9.4e-06 2_[+2]_83 98 1.1e-05 40_[+2]_45 40 1.4e-05 28_[+2]_57 27 1.4e-05 17_[+2]_68 49 1.6e-05 29_[+2]_56 47 1.6e-05 3_[+2]_82 53 2.2e-05 66_[+2]_19 52 2.2e-05 15_[+2]_70 60 2.5e-05 38_[+2]_47 63 4.9e-05 12_[+2]_73 81 5.4e-05 22_[+2]_63 73 6e-05 31_[+2]_54 94 6.6e-05 44_[+2]_41 88 8.1e-05 1_[+2]_84 65 8.1e-05 51_[+2]_34 7 9.8e-05 32_[+2]_53 91 0.00011 63_[+2]_22 35 0.00014 31_[+2]_54 6 0.00014 59_[+2]_26 99 0.00017 1_[+2]_84 84 0.00017 70_[+2]_15 32 0.00017 32_[+2]_53 87 0.00018 [+2]_85 69 0.0002 36_[+2]_49 70 0.00023 29_[+2]_56 43 0.00023 74_[+2]_11 38 0.00025 16_[+2]_69 31 0.00032 1_[+2]_84 95 0.00035 58_[+2]_27 76 0.00035 31_[+2]_54 61 0.00035 50_[+2]_35 58 0.0005 60_[+2]_25 83 0.00061 13_[+2]_72 22 0.00061 2_[+2]_83 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif BCTYYTTTYTTKTNW MEME-2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF BCTYYTTTYTTKTNW width=15 seqs=45 12 ( 10) CCTTTTTTCTTTTGT 1 21 ( 36) CCTCCTTCCTCTTAT 1 1 ( 33) GCTCTTTTTTTGTGT 1 39 ( 19) GCTTCTTTTTTTTGC 1 74 ( 1) CCCCTATCCTTTTCT 1 72 ( 38) TCTTCTTTCATTTAT 1 75 ( 1) CCCCTTTCCTTTCGT 1 92 ( 33) GCTTTTTTCTTTTTT 1 67 ( 3) CCTTCCTCCCTTTTC 1 96 ( 29) CCTCCTTCTCTCTGA 1 28 ( 1) TCTGCTTTCATTTCA 1 68 ( 3) TCTCCTTTATTTTAC 1 98 ( 41) CCCACTTTTTTGTGA 1 40 ( 29) TCTTTTTTTATGTGT 1 27 ( 18) CTCCCTTTATTGTAT 1 49 ( 30) TCTGTTTTCTTTTTT 1 47 ( 4) GCCCCTTTCACTTCA 1 53 ( 67) CCTATTTTTTTGTGC 1 52 ( 16) TTTTCCTCCTTGTCA 1 60 ( 39) GCTTTTTTCTTGACT 1 63 ( 13) TCTTTTTTATTGTTT 1 81 ( 23) CCTCCATTTCCTTAT 1 73 ( 32) ATTCCTTTTTTTTCA 1 94 ( 45) GTTTTTTCTCTTTGT 1 88 ( 2) TCCCCCTCAATTTTT 1 65 ( 52) ACTTCTTGCATTTAT 1 7 ( 33) CTCGTTTTTATTTGT 1 91 ( 64) CCGTTTTTTATTTGC 1 35 ( 32) CCATCCTTTTTGTAT 1 6 ( 60) GCGTTTTTCTGTTCT 1 99 ( 2) TCTCCTTTCAGCTAA 1 84 ( 71) GTTTTTTTATTTTCA 1 32 ( 33) TCCACTTACTTGTCT 1 87 ( 1) TCTCTATGATTTTGT 1 69 ( 37) CTTTCTTTCAGGAGT 1 70 ( 30) CTTGCTTTTTTGAAT 1 43 ( 75) ACTTTTTCACTGTGA 1 38 ( 17) CTTTTTTTGTTTTCA 1 31 ( 2) TCCCCCTGTCGGTAT 1 95 ( 59) TTTTCATTATTTTTT 1 76 ( 32) GCCGTTTGCATGTAA 1 61 ( 51) TTTCCCTCCTTTATA 1 58 ( 61) TTTTCATTCATTCGC 1 83 ( 14) ATTCCATTTTTGTTA 1 22 ( 3) CTTACTTTTCTATGT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif BCTYYTTTYTTKTNW MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 8600 bayes= 7.9516 E= 3.2e-008 -196 144 4 6 -1214 230 -1214 -4 -396 67 -213 115 -196 135 -81 48 -1214 205 -1214 40 -138 -7 -1214 120 -1214 -1214 -1214 165 -396 67 -113 106 -96 167 -313 15 -38 16 -1214 85 -1214 -107 -113 140 -396 -165 87 85 -196 -165 -1214 144 -50 67 87 -85 -26 -7 -1214 85 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif BCTYYTTTYTTKTNW MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 45 E= 3.2e-008 0.088889 0.377778 0.200000 0.333333 0.000000 0.688889 0.000000 0.311111 0.022222 0.222222 0.044444 0.711111 0.088889 0.355556 0.111111 0.444444 0.000000 0.577778 0.000000 0.422222 0.133333 0.133333 0.000000 0.733333 0.000000 0.000000 0.000000 1.000000 0.022222 0.222222 0.088889 0.666667 0.177778 0.444444 0.022222 0.355556 0.266667 0.155556 0.000000 0.577778 0.000000 0.066667 0.088889 0.844444 0.022222 0.044444 0.355556 0.577778 0.088889 0.044444 0.000000 0.866667 0.244444 0.222222 0.355556 0.177778 0.288889 0.133333 0.000000 0.577778 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif BCTYYTTTYTTKTNW MEME-2 regular expression -------------------------------------------------------------------------------- [CTG][CT][TC][TC][CT]TT[TC][CT][TA]T[TG]T[GAC][TA] -------------------------------------------------------------------------------- Time 11.27 secs. ******************************************************************************** ******************************************************************************** MOTIF MYCRRCHRMWTTDCYTTRCGR MEME-3 width = 21 sites = 9 llr = 140 E-value = 8.2e+000 ******************************************************************************** -------------------------------------------------------------------------------- Motif MYCRRCHRMWTTDCYTTRCGR MEME-3 Description -------------------------------------------------------------------------------- Simplified A 4:267:3633::2:11:4116 pos.-specific C 677::9417:11:84::172: probability G :::33::3:1::4:1::4174 matrix T :311:12::6993239a:1:: bits 2.8 2.6 2.3 * 2.0 * Relative 1.7 * * * Entropy 1.4 * * * * * (22.4 bits) 1.1 *** * * ** * ** ** 0.9 *** ** * ** * ** *** 0.6 ********* ** ******** 0.3 ********************* 0.0 --------------------- Multilevel CCCAACCACTTTGCCTTACGA consensus ATAGG AGAA TTT G CG sequence T A -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif MYCRRCHRMWTTDCYTTRCGR MEME-3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 84 43 1.78e-11 TATGCCAATT CCAAACCACTTTTCCTTGCGG GAAAGTGGTT 13 16 9.37e-10 TGCTGACACA CCCGGCCGCTTTGCCATGGCA AGGTGTTCAG 58 31 4.41e-09 ATGAAGTTAA ATCAACAGCATTACCTTACGA TCAAAGGAAT 34 41 1.31e-08 TCTCTATATC CTCTACTGCATCTCCTTGCGA CTTCATCCGC 51 69 8.72e-08 TAGATTTTGA CCCAACCAATTTATTTTAAGG AGACCGATTC 67 57 1.19e-07 ACAGTTGAGC ACCGGCTCATCTGTTTTGCGA AACAGCCAGA 61 29 1.28e-07 TCAATCATCT CCAAGCCAAGTTGCGTTATGG TTTTCCCTCC 9 41 1.49e-07 CACTTTTTTC ACTAACAACATTGCTTTACAA TTAAAAACAA 86 53 5.45e-07 CAAATTGTTA ATCGATAACTTTTCATTCCCG ATATTAAAAA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif MYCRRCHRMWTTDCYTTRCGR MEME-3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 84 1.8e-11 42_[+3]_37 13 9.4e-10 15_[+3]_64 58 4.4e-09 30_[+3]_49 34 1.3e-08 40_[+3]_39 51 8.7e-08 68_[+3]_11 67 1.2e-07 56_[+3]_23 61 1.3e-07 28_[+3]_51 9 1.5e-07 40_[+3]_39 86 5.5e-07 52_[+3]_27 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif MYCRRCHRMWTTDCYTTRCGR MEME-3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF MYCRRCHRMWTTDCYTTRCGR width=21 seqs=9 84 ( 43) CCAAACCACTTTTCCTTGCGG 1 13 ( 16) CCCGGCCGCTTTGCCATGGCA 1 58 ( 31) ATCAACAGCATTACCTTACGA 1 34 ( 41) CTCTACTGCATCTCCTTGCGA 1 51 ( 69) CCCAACCAATTTATTTTAAGG 1 67 ( 57) ACCGGCTCATCTGTTTTGCGA 1 61 ( 29) CCAAGCCAAGTTGCGTTATGG 1 9 ( 41) ACTAACAACATTGCTTTACAA 1 86 ( 53) ATCGATAACTTTTCATTCCCG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif MYCRRCHRMWTTDCYTTRCGR MEME-3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 8000 bayes= 9.92868 E= 8.2e+000 36 199 -982 -982 -982 225 -982 6 -64 225 -982 -152 68 -982 78 -152 94 -982 78 -982 -982 267 -982 -152 -6 167 -982 -52 68 -33 78 -982 -6 225 -982 -982 -6 -982 -81 80 -982 -33 -982 147 -982 -33 -982 147 -64 -982 119 6 -982 248 -982 -52 -164 167 -81 6 -164 -982 -982 147 -982 -982 -982 164 36 -33 119 -982 -164 225 -81 -152 -164 67 178 -982 68 -982 119 -982 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif MYCRRCHRMWTTDCYTTRCGR MEME-3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 9 E= 8.2e+000 0.444444 0.555556 0.000000 0.000000 0.000000 0.666667 0.000000 0.333333 0.222222 0.666667 0.000000 0.111111 0.555556 0.000000 0.333333 0.111111 0.666667 0.000000 0.333333 0.000000 0.000000 0.888889 0.000000 0.111111 0.333333 0.444444 0.000000 0.222222 0.555556 0.111111 0.333333 0.000000 0.333333 0.666667 0.000000 0.000000 0.333333 0.000000 0.111111 0.555556 0.000000 0.111111 0.000000 0.888889 0.000000 0.111111 0.000000 0.888889 0.222222 0.000000 0.444444 0.333333 0.000000 0.777778 0.000000 0.222222 0.111111 0.444444 0.111111 0.333333 0.111111 0.000000 0.000000 0.888889 0.000000 0.000000 0.000000 1.000000 0.444444 0.111111 0.444444 0.000000 0.111111 0.666667 0.111111 0.111111 0.111111 0.222222 0.666667 0.000000 0.555556 0.000000 0.444444 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif MYCRRCHRMWTTDCYTTRCGR MEME-3 regular expression -------------------------------------------------------------------------------- [CA][CT][CA][AG][AG]C[CAT][AG][CA][TA]TT[GTA][CT][CT]TT[AG]C[GC][AG] -------------------------------------------------------------------------------- Time 15.98 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 1 9.03e-05 32_[+2(1.55e-06)]_53 2 7.76e-02 100 3 2.48e-01 100 4 5.08e-01 100 5 9.18e-02 100 6 2.38e-03 100 7 5.46e-02 32_[+2(9.79e-05)]_53 8 9.45e-01 100 9 1.14e-04 40_[+3(1.49e-07)]_39 10 1.72e-01 100 11 6.69e-01 100 12 9.68e-05 9_[+2(8.76e-08)]_76 13 9.68e-08 15_[+3(9.37e-10)]_64 14 3.44e-02 100 15 1.49e-01 100 16 7.38e-01 100 17 8.51e-01 100 18 1.33e-01 100 19 6.63e-02 100 20 1.31e-01 100 21 1.18e-03 35_[+2(8.24e-07)]_50 22 7.53e-03 100 23 4.02e-01 100 24 3.35e-01 100 25 2.55e-01 100 26 5.08e-01 100 27 9.86e-04 17_[+2(1.39e-05)]_68 28 4.17e-04 [+2(8.06e-06)]_85 29 7.19e-03 100 30 6.14e-01 100 31 4.87e-02 100 32 4.66e-02 100 33 8.64e-02 100 34 3.37e-07 40_[+3(1.31e-08)]_39 35 1.53e-02 100 36 3.58e-01 100 37 1.12e-01 100 38 1.29e-03 100 39 3.94e-05 18_[+2(1.84e-06)]_67 40 2.47e-03 28_[+2(1.39e-05)]_57 41 4.44e-01 100 42 3.35e-01 100 43 7.92e-02 100 44 2.38e-01 100 45 3.34e-01 100 46 3.66e-01 100 47 5.80e-04 3_[+2(1.56e-05)]_82 48 4.40e-01 100 49 1.15e-02 29_[+2(1.56e-05)]_56 50 6.41e-02 100 51 9.97e-05 68_[+3(8.72e-08)]_11 52 8.87e-04 15_[+2(2.22e-05)]_70 53 5.50e-04 66_[+2(2.22e-05)]_19 54 8.84e-01 100 55 1.30e-01 100 56 1.42e-01 100 57 1.47e-01 100 58 9.21e-07 30_[+3(4.41e-09)]_49 59 7.80e-01 100 60 3.41e-04 38_[+2(2.51e-05)]_47 61 1.84e-05 28_[+3(1.28e-07)]_51 62 6.54e-01 100 63 5.96e-03 12_[+2(4.86e-05)]_73 64 7.43e-02 100 65 4.67e-03 51_[+2(8.12e-05)]_34 66 2.07e-02 100 67 4.31e-08 2_[+2(4.73e-06)]_39_[+3(1.19e-07)]_\ 23 68 2.94e-04 2_[+2(9.38e-06)]_83 69 1.14e-02 100 70 8.78e-03 100 71 2.95e-01 100 72 1.64e-03 37_[+2(2.16e-06)]_48 73 2.34e-02 31_[+2(5.96e-05)]_54 74 1.82e-03 [+2(2.16e-06)]_85 75 1.54e-03 [+2(3.52e-06)]_85 76 9.58e-02 100 77 8.68e-01 100 78 5.01e-01 100 79 8.64e-02 100 80 2.39e-01 100 81 1.66e-03 22_[+2(5.37e-05)]_63 82 1.12e-01 100 83 1.36e-01 100 84 2.91e-10 42_[+3(1.78e-11)]_37 85 2.19e-01 100 86 3.49e-04 52_[+3(5.45e-07)]_27 87 2.08e-02 100 88 8.49e-03 1_[+2(8.12e-05)]_84 89 8.62e-01 100 90 5.54e-01 100 91 1.99e-03 100 92 4.90e-04 32_[+2(4.73e-06)]_53 93 7.72e-01 100 94 3.27e-02 44_[+2(6.64e-05)]_41 95 1.12e-01 100 96 3.10e-04 28_[+2(8.06e-06)]_57 97 1.80e-01 100 98 9.05e-03 40_[+2(1.07e-05)]_45 99 5.33e-02 100 100 1.61e-01 100 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (3) found. ******************************************************************************** CPU: kodomo ********************************************************************************