******************************************************************************** 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_Ideonella_dechlorat 1.0000 100 seq2_Ideonella_dechlorat 1.0000 100 seq3_Ideonella_dechlorat 1.0000 100 seq4_Ideonella_dechlorat 1.0000 100 seq5_Ideonella_dechlorat 1.0000 100 seq6_Ideonella_dechlorat 1.0000 100 seq7_Ideonella_dechlorat 1.0000 100 seq8_Ideonella_dechlorat 1.0000 100 seq9_Ideonella_dechlorat 1.0000 100 seq10_Ideonella_dechlora 1.0000 100 seq11_Ideonella_dechlora 1.0000 100 seq12_Ideonella_dechlora 1.0000 100 seq13_Ideonella_dechlora 1.0000 100 seq14_Ideonella_dechlora 1.0000 100 seq15_Ideonella_dechlora 1.0000 100 seq16_Ideonella_dechlora 1.0000 100 seq17_Ideonella_dechlora 1.0000 100 seq18_Ideonella_dechlora 1.0000 100 seq19_Ideonella_dechlora 1.0000 100 seq20_Ideonella_dechlora 1.0000 100 seq21_Ideonella_dechlora 1.0000 100 seq22_Ideonella_dechlora 1.0000 100 seq23_Ideonella_dechlora 1.0000 100 seq24_Ideonella_dechlora 1.0000 100 seq25_Ideonella_dechlora 1.0000 100 seq26_Ideonella_dechlora 1.0000 100 seq27_Ideonella_dechlora 1.0000 100 seq28_Ideonella_dechlora 1.0000 100 seq29_Ideonella_dechlora 1.0000 100 seq30_Ideonella_dechlora 1.0000 100 seq31_Ideonella_dechlora 1.0000 100 seq32_Ideonella_dechlora 1.0000 100 seq33_Ideonella_dechlora 1.0000 100 seq34_Ideonella_dechlora 1.0000 100 seq35_Ideonella_dechlora 1.0000 100 seq36_Ideonella_dechlora 1.0000 100 seq37_Ideonella_dechlora 1.0000 100 seq38_Ideonella_dechlora 1.0000 100 seq39_Ideonella_dechlora 1.0000 100 seq40_Ideonella_dechlora 1.0000 100 seq41_Ideonella_dechlora 1.0000 100 seq42_Ideonella_dechlora 1.0000 100 seq43_Ideonella_dechlora 1.0000 100 seq44_Ideonella_dechlora 1.0000 100 seq45_Ideonella_dechlora 1.0000 100 seq46_Ideonella_dechlora 1.0000 100 seq47_Ideonella_dechlora 1.0000 100 seq49_Ideonella_dechlora 1.0000 100 seq50_Ideonella_dechlora 1.0000 100 seq51_Ideonella_dechlora 1.0000 100 seq52_Ideonella_dechlora 1.0000 100 seq53_Ideonella_dechlora 1.0000 100 seq54_Ideonella_dechlora 1.0000 100 seq55_Ideonella_dechlora 1.0000 100 seq56_Ideonella_dechlora 1.0000 100 seq57_Ideonella_dechlora 1.0000 100 seq58_Ideonella_dechlora 1.0000 100 seq59_Ideonella_dechlora 1.0000 100 seq60_Ideonella_dechlora 1.0000 100 seq61_Ideonella_dechlora 1.0000 100 seq62_Ideonella_dechlora 1.0000 100 seq63_Ideonella_dechlora 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 -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= 62 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= 6200 N= 62 sample: seed= 0 hsfrac= 0 searchsize= 6200 norand= no csites= 1000 Letter frequencies in dataset: A 0.171 C 0.337 G 0.313 T 0.179 Background letter frequencies (from file dataset with add-one prior applied): A 0.171 C 0.337 G 0.313 T 0.179 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF CTAMAWTSAAMRGTTCGVKKHHAW MEME-1 width = 24 sites = 9 llr = 150 E-value = 2.5e-002 ******************************************************************************** -------------------------------------------------------------------------------- Motif CTAMAWTSAAMRGTTCGVKKHHAW MEME-1 Description -------------------------------------------------------------------------------- Simplified A 1:93841:7833:2:::3::2277 pos.-specific C 9::621231241:218241:442: probability G :1:::1:7::169::16234:11: matrix T :911:37:2:1:16912:6632:3 bits 2.5 2.3 2.0 * 1.8 ** * Relative 1.5 ** * * * * Entropy 1.3 *** * ** * * * (24.0 bits) 1.0 *** * * ** * * * ** 0.8 ***** **** **** ** ** 0.5 ********** ********** ** 0.3 ************************ 0.0 ------------------------ Multilevel CTACAATGAACGGTTCGCTTCCAA consensus ACTCCTCAA A CAGGTACT sequence C TG AT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTAMAWTSAAMRGTTCGVKKHHAW MEME-1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------------------ seq14_Ideonella_dechlora 5 2.00e-12 GAAC CTATAATGAAAGGTTCCATTTCAT CCCCTCGGGT seq62_Ideonella_dechlora 1 8.46e-12 . CTAAAATGAACGGTTCGCTTCCCT GTCCCGGCTC seq53_Ideonella_dechlora 53 1.10e-09 ACACCAATCG CTACATCGACCAGTTCTCGGTCAA TGGCGCAGGG seq1_Ideonella_dechlorat 30 1.10e-09 GGCGTCGGCG CTACCATGTACAGATCGCGGAAAA ACACTTCTGC seq61_Ideonella_dechlora 46 1.24e-08 TCTTGACGTG CTTCATACAATGGTCCGATTTTAA GGGGCCCACC seq27_Ideonella_dechlora 38 1.17e-07 GGGATTGGGG CGACATTCTACGGATGCCGGCCAA CGCCAGCTGA seq13_Ideonella_dechlora 34 1.43e-07 TTCGATTGAA ATACCGCGAAAAGCTCGGTTATCA TCCATTCGCT seq41_Ideonella_dechlora 62 1.96e-07 CCCCCCGGTG CTAAACTCAAACGCTTTGTTCAGT CCCGTTGACG seq42_Ideonella_dechlora 66 2.09e-07 TGCGGGAAAC CTAAAATGCCGGTTTCGACGCGAA ACGCAACGAC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTAMAWTSAAMRGTTCGVKKHHAW MEME-1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- seq14_Ideonella_dechlora 2e-12 4_[+1]_72 seq62_Ideonella_dechlora 8.5e-12 [+1]_76 seq53_Ideonella_dechlora 1.1e-09 52_[+1]_24 seq1_Ideonella_dechlorat 1.1e-09 29_[+1]_47 seq61_Ideonella_dechlora 1.2e-08 45_[+1]_31 seq27_Ideonella_dechlora 1.2e-07 37_[+1]_39 seq13_Ideonella_dechlora 1.4e-07 33_[+1]_43 seq41_Ideonella_dechlora 2e-07 61_[+1]_15 seq42_Ideonella_dechlora 2.1e-07 65_[+1]_11 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTAMAWTSAAMRGTTCGVKKHHAW MEME-1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF CTAMAWTSAAMRGTTCGVKKHHAW width=24 seqs=9 seq14_Ideonella_dechlora ( 5) CTATAATGAAAGGTTCCATTTCAT 1 seq62_Ideonella_dechlora ( 1) CTAAAATGAACGGTTCGCTTCCCT 1 seq53_Ideonella_dechlora ( 53) CTACATCGACCAGTTCTCGGTCAA 1 seq1_Ideonella_dechlorat ( 30) CTACCATGTACAGATCGCGGAAAA 1 seq61_Ideonella_dechlora ( 46) CTTCATACAATGGTCCGATTTTAA 1 seq27_Ideonella_dechlora ( 38) CGACATTCTACGGATGCCGGCCAA 1 seq13_Ideonella_dechlora ( 34) ATACCGCGAAAAGCTCGGTTATCA 1 seq41_Ideonella_dechlora ( 62) CTAAACTCAAACGCTTTGTTCAGT 1 seq42_Ideonella_dechlora ( 66) CTAAAATGCCGGTTTCGACGCGAA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTAMAWTSAAMRGTTCGVKKHHAW MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 24 n= 4774 bayes= 9.18288 E= 2.5e-002 -62 140 -982 -982 -982 -982 -149 231 238 -982 -982 -68 96 72 -982 -68 218 -60 -982 -982 138 -160 -149 90 -62 -60 -982 190 -982 -2 109 -982 196 -160 -982 32 218 -60 -982 -982 96 40 -149 -68 96 -160 83 -982 -982 -982 150 -68 38 -60 -982 164 -982 -160 -982 231 -982 121 -149 -68 -982 -60 83 32 96 40 -50 -982 -982 -160 9 164 -982 -982 50 164 38 40 -982 90 38 40 -149 32 196 -60 -149 -982 196 -982 -982 90 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTAMAWTSAAMRGTTCGVKKHHAW MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 24 nsites= 9 E= 2.5e-002 0.111111 0.888889 0.000000 0.000000 0.000000 0.000000 0.111111 0.888889 0.888889 0.000000 0.000000 0.111111 0.333333 0.555556 0.000000 0.111111 0.777778 0.222222 0.000000 0.000000 0.444444 0.111111 0.111111 0.333333 0.111111 0.222222 0.000000 0.666667 0.000000 0.333333 0.666667 0.000000 0.666667 0.111111 0.000000 0.222222 0.777778 0.222222 0.000000 0.000000 0.333333 0.444444 0.111111 0.111111 0.333333 0.111111 0.555556 0.000000 0.000000 0.000000 0.888889 0.111111 0.222222 0.222222 0.000000 0.555556 0.000000 0.111111 0.000000 0.888889 0.000000 0.777778 0.111111 0.111111 0.000000 0.222222 0.555556 0.222222 0.333333 0.444444 0.222222 0.000000 0.000000 0.111111 0.333333 0.555556 0.000000 0.000000 0.444444 0.555556 0.222222 0.444444 0.000000 0.333333 0.222222 0.444444 0.111111 0.222222 0.666667 0.222222 0.111111 0.000000 0.666667 0.000000 0.000000 0.333333 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTAMAWTSAAMRGTTCGVKKHHAW MEME-1 regular expression -------------------------------------------------------------------------------- CTA[CA][AC][AT][TC][GC][AT][AC][CA][GA]G[TAC]TC[GCT][CAG][TG][TG][CTA][CAT][AC][AT] -------------------------------------------------------------------------------- Time 2.69 secs. ******************************************************************************** ******************************************************************************** MOTIF AATCCGCSAYABTC MEME-2 width = 14 sites = 13 llr = 136 E-value = 4.1e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif AATCCGCSAYABTC MEME-2 Description -------------------------------------------------------------------------------- Simplified A 89:::2:17:71:: pos.-specific C :::7728413:3:8 probability G 2:21361522:31: matrix T :182::21:53392 bits 2.5 2.3 2.0 * * 1.8 *** * Relative 1.5 *** * * Entropy 1.3 *** * * (15.1 bits) 1.0 *** * * ** 0.8 ***** * *** ** 0.5 ******* *** ** 0.3 *********** ** 0.0 -------------- Multilevel AATCCGCGATACTC consensus TGA CGCTG sequence T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AATCCGCSAYABTC MEME-2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------------- seq37_Ideonella_dechlora 55 9.96e-08 CACTGTCAAA AATCCGCTATACTC GATAGTCTTT seq8_Ideonella_dechlorat 32 5.08e-07 GGAGCTGTGC AATCCGCCACTGTC GCACATCCCC seq11_Ideonella_dechlora 46 8.18e-07 CCGATGACAT AATCCGCGGTTCTC AGCCCGGTCG seq49_Ideonella_dechlora 70 2.66e-06 ATGGTTGTCA AATCCGCCGCATTT GCTCCGGACG seq32_Ideonella_dechlora 11 3.23e-06 CGGCCGGGCC GATCGGCGATAATC TTGCCCCTTC seq23_Ideonella_dechlora 48 4.70e-06 TGCAGGATGA AATCGATCAGAGTC GGCAGCAGGT seq55_Ideonella_dechlora 54 5.15e-06 CACATGGGAC AATTCGCGCTTGTC CAACACTTGA seq54_Ideonella_dechlora 43 7.33e-06 CATTGCGGCA AAGTGGCGATACTT GGCCAACTTC seq19_Ideonella_dechlora 16 1.30e-05 CTGAGGCCGG AATCCCGCAGATTC CACACGAGGG seq27_Ideonella_dechlora 79 1.40e-05 TGACCGGGCC AAGCCACGATATGC TGCGCGCA seq13_Ideonella_dechlora 10 1.40e-05 GCCGGTAGC AATCGATAACTGTC TTCGATTGAA seq30_Ideonella_dechlora 41 1.89e-05 GTTCCGGTTC GATGCGCGACACTC TGTGCCTGTT seq35_Ideonella_dechlora 40 2.19e-05 CGCCCGAATG ATTTCCCCGTATTC GCATCGCTCA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AATCCGCSAYABTC MEME-2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- seq37_Ideonella_dechlora 1e-07 54_[+2]_32 seq8_Ideonella_dechlorat 5.1e-07 31_[+2]_55 seq11_Ideonella_dechlora 8.2e-07 45_[+2]_41 seq49_Ideonella_dechlora 2.7e-06 69_[+2]_17 seq32_Ideonella_dechlora 3.2e-06 10_[+2]_76 seq23_Ideonella_dechlora 4.7e-06 47_[+2]_39 seq55_Ideonella_dechlora 5.2e-06 53_[+2]_33 seq54_Ideonella_dechlora 7.3e-06 42_[+2]_44 seq19_Ideonella_dechlora 1.3e-05 15_[+2]_71 seq27_Ideonella_dechlora 1.4e-05 78_[+2]_8 seq13_Ideonella_dechlora 1.4e-05 9_[+2]_77 seq30_Ideonella_dechlora 1.9e-05 40_[+2]_46 seq35_Ideonella_dechlora 2.2e-05 39_[+2]_47 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AATCCGCSAYABTC MEME-2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF AATCCGCSAYABTC width=14 seqs=13 seq37_Ideonella_dechlora ( 55) AATCCGCTATACTC 1 seq8_Ideonella_dechlorat ( 32) AATCCGCCACTGTC 1 seq11_Ideonella_dechlora ( 46) AATCCGCGGTTCTC 1 seq49_Ideonella_dechlora ( 70) AATCCGCCGCATTT 1 seq32_Ideonella_dechlora ( 11) GATCGGCGATAATC 1 seq23_Ideonella_dechlora ( 48) AATCGATCAGAGTC 1 seq55_Ideonella_dechlora ( 54) AATTCGCGCTTGTC 1 seq54_Ideonella_dechlora ( 43) AAGTGGCGATACTT 1 seq19_Ideonella_dechlora ( 16) AATCCCGCAGATTC 1 seq27_Ideonella_dechlora ( 79) AAGCCACGATATGC 1 seq13_Ideonella_dechlora ( 10) AATCGATAACTGTC 1 seq30_Ideonella_dechlora ( 41) GATGCGCGACACTC 1 seq35_Ideonella_dechlora ( 40) ATTTCCCCGTATTC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AATCCGCSAYABTC MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 14 n= 5394 bayes= 9.22481 E= 4.1e+001 230 -1035 -103 -1035 243 -1035 -1035 -121 -1035 -1035 -103 224 -1035 104 -202 37 -1035 104 -3 -1035 43 -113 97 -1035 -1035 119 -202 -22 -115 19 56 -121 202 -213 -44 -1035 -1035 -13 -103 159 202 -1035 -1035 78 -115 -13 -3 78 -1035 -1035 -202 237 -1035 133 -1035 -22 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AATCCGCSAYABTC MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 14 nsites= 13 E= 4.1e+001 0.846154 0.000000 0.153846 0.000000 0.923077 0.000000 0.000000 0.076923 0.000000 0.000000 0.153846 0.846154 0.000000 0.692308 0.076923 0.230769 0.000000 0.692308 0.307692 0.000000 0.230769 0.153846 0.615385 0.000000 0.000000 0.769231 0.076923 0.153846 0.076923 0.384615 0.461538 0.076923 0.692308 0.076923 0.230769 0.000000 0.000000 0.307692 0.153846 0.538462 0.692308 0.000000 0.000000 0.307692 0.076923 0.307692 0.307692 0.307692 0.000000 0.000000 0.076923 0.923077 0.000000 0.846154 0.000000 0.153846 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AATCCGCSAYABTC MEME-2 regular expression -------------------------------------------------------------------------------- AAT[CT][CG][GA]C[GC][AG][TC][AT][CGT]TC -------------------------------------------------------------------------------- Time 5.19 secs. ******************************************************************************** ******************************************************************************** MOTIF TGKYNKYWTGKKGAHGGRAWSRRRMTD MEME-3 width = 27 sites = 7 llr = 128 E-value = 1.7e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif TGKYNKYWTGKKGAHGGRAWSRRRMTD MEME-3 Description -------------------------------------------------------------------------------- Simplified A :::131:3::1::a4:169416343:3 pos.-specific C 1:141:61:3:1::3::1:14:1:6:: probability G :a313411:764a::993113446113 matrix T 9:633434a:34::31:::31:1::94 bits 2.5 * * 2.3 * * 2.0 * * 1.8 ** * ** * * Relative 1.5 ** * ** * * Entropy 1.3 ** * ** ** * * * (26.4 bits) 1.0 ** * ** ** * * * * 0.8 *** * *** ******* * * ** 0.5 *** *************** * **** 0.3 ******************** ****** 0.0 --------------------------- Multilevel TGTCAGCTTGGGGAAGGAAACAGGCTT consensus GTGTTA CTT C G TGGAAA A sequence T T G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TGKYNKYWTGKKGAHGGRAWSRRRMTD MEME-3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------------- seq4_Ideonella_dechlorat 68 9.01e-11 AAGCTCCACA TGGTCTCTTGGTGATTGAAAGGAGCTT CCCCCA seq39_Ideonella_dechlora 71 2.02e-10 TCTTGGTTTG TGTCTTCATGTTGAAGGGATAATACGA GGA seq38_Ideonella_dechlora 20 3.47e-10 TCCTCAAGCC TGTGAACTTGGGGACGAAAACAGGGTT GCTCGGTCTA seq16_Ideonella_dechlora 13 1.25e-09 GGAAAGGCGA TGCAAGCATCGTGAAGGAACCGAACTG CCGGAATTAT seq56_Ideonella_dechlora 66 7.58e-09 ACCCCAGGCC TGTCTGTCTGTCGACGGAAGGACAATG ACTGTCGA seq27_Ideonella_dechlora 7 1.24e-08 TGGTCT CGGTGGTGTGAGGAAGGGAACGGGATT GGGGCGACAT seq2_Ideonella_dechlorat 32 1.24e-08 TGGCGGGCAG TGTCGTGTTCGGGATGGCGTTAGGCTA AGGGCTGCGG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TGKYNKYWTGKKGAHGGRAWSRRRMTD MEME-3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- seq4_Ideonella_dechlorat 9e-11 67_[+3]_6 seq39_Ideonella_dechlora 2e-10 70_[+3]_3 seq38_Ideonella_dechlora 3.5e-10 19_[+3]_54 seq16_Ideonella_dechlora 1.2e-09 12_[+3]_61 seq56_Ideonella_dechlora 7.6e-09 65_[+3]_8 seq27_Ideonella_dechlora 1.2e-08 6_[+3]_67 seq2_Ideonella_dechlorat 1.2e-08 31_[+3]_42 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TGKYNKYWTGKKGAHGGRAWSRRRMTD MEME-3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF TGKYNKYWTGKKGAHGGRAWSRRRMTD width=27 seqs=7 seq4_Ideonella_dechlorat ( 68) TGGTCTCTTGGTGATTGAAAGGAGCTT 1 seq39_Ideonella_dechlora ( 71) TGTCTTCATGTTGAAGGGATAATACGA 1 seq38_Ideonella_dechlora ( 20) TGTGAACTTGGGGACGAAAACAGGGTT 1 seq16_Ideonella_dechlora ( 13) TGCAAGCATCGTGAAGGAACCGAACTG 1 seq56_Ideonella_dechlora ( 66) TGTCTGTCTGTCGACGGAAGGACAATG 1 seq27_Ideonella_dechlora ( 7) CGGTGGTGTGAGGAAGGGAACGGGATT 1 seq2_Ideonella_dechlorat ( 32) TGTCGTGTTCGGGATGGCGTTAGGCTA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TGKYNKYWTGKKGAHGGRAWSRRRMTD MEME-3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 27 n= 4588 bayes= 9.96057 E= 1.7e+002 -945 -123 -945 226 -945 -945 167 -945 -945 -123 -13 168 -26 35 -113 68 74 -123 -13 68 -26 -945 45 126 -945 76 -113 68 74 -123 -113 126 -945 -945 -945 248 -945 -24 119 -945 -26 -945 87 68 -945 -123 45 126 -945 -945 167 -945 254 -945 -945 -945 132 -24 -945 68 -945 -945 145 -32 -26 -945 145 -945 174 -123 -13 -945 232 -945 -113 -945 132 -123 -113 68 -26 35 -13 -32 174 -945 45 -945 74 -123 45 -32 132 -945 87 -945 74 76 -113 -945 -945 -945 -113 226 74 -945 -13 126 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TGKYNKYWTGKKGAHGGRAWSRRRMTD MEME-3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 27 nsites= 7 E= 1.7e+002 0.000000 0.142857 0.000000 0.857143 0.000000 0.000000 1.000000 0.000000 0.000000 0.142857 0.285714 0.571429 0.142857 0.428571 0.142857 0.285714 0.285714 0.142857 0.285714 0.285714 0.142857 0.000000 0.428571 0.428571 0.000000 0.571429 0.142857 0.285714 0.285714 0.142857 0.142857 0.428571 0.000000 0.000000 0.000000 1.000000 0.000000 0.285714 0.714286 0.000000 0.142857 0.000000 0.571429 0.285714 0.000000 0.142857 0.428571 0.428571 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.428571 0.285714 0.000000 0.285714 0.000000 0.000000 0.857143 0.142857 0.142857 0.000000 0.857143 0.000000 0.571429 0.142857 0.285714 0.000000 0.857143 0.000000 0.142857 0.000000 0.428571 0.142857 0.142857 0.285714 0.142857 0.428571 0.285714 0.142857 0.571429 0.000000 0.428571 0.000000 0.285714 0.142857 0.428571 0.142857 0.428571 0.000000 0.571429 0.000000 0.285714 0.571429 0.142857 0.000000 0.000000 0.000000 0.142857 0.857143 0.285714 0.000000 0.285714 0.428571 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TGKYNKYWTGKKGAHGGRAWSRRRMTD MEME-3 regular expression -------------------------------------------------------------------------------- TG[TG][CT][AGT][GT][CT][TA]T[GC][GT][GT]GA[ACT]GG[AG]A[AT][CG][AG][GA][GA][CA]T[TAG] -------------------------------------------------------------------------------- Time 7.62 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- seq1_Ideonella_dechlorat 2.08e-06 29_[+1(1.10e-09)]_47 seq2_Ideonella_dechlorat 2.67e-05 31_[+3(1.24e-08)]_42 seq3_Ideonella_dechlorat 9.71e-01 100 seq4_Ideonella_dechlorat 7.58e-07 67_[+3(9.01e-11)]_6 seq5_Ideonella_dechlorat 6.51e-01 100 seq6_Ideonella_dechlorat 8.45e-01 100 seq7_Ideonella_dechlorat 6.83e-01 100 seq8_Ideonella_dechlorat 2.31e-03 31_[+2(5.08e-07)]_55 seq9_Ideonella_dechlorat 5.47e-01 100 seq10_Ideonella_dechlora 5.18e-01 100 seq11_Ideonella_dechlora 2.28e-03 45_[+2(8.18e-07)]_41 seq12_Ideonella_dechlora 9.29e-01 100 seq13_Ideonella_dechlora 1.46e-06 9_[+2(1.40e-05)]_10_[+1(1.43e-07)]_\ 43 seq14_Ideonella_dechlora 2.25e-08 4_[+1(2.00e-12)]_72 seq15_Ideonella_dechlora 4.15e-01 100 seq16_Ideonella_dechlora 5.87e-06 12_[+3(1.25e-09)]_61 seq17_Ideonella_dechlora 2.82e-01 100 seq18_Ideonella_dechlora 9.45e-01 100 seq19_Ideonella_dechlora 6.54e-03 15_[+2(1.30e-05)]_71 seq20_Ideonella_dechlora 4.56e-01 100 seq21_Ideonella_dechlora 3.75e-01 100 seq22_Ideonella_dechlora 1.63e-01 100 seq23_Ideonella_dechlora 4.46e-04 47_[+2(4.70e-06)]_39 seq24_Ideonella_dechlora 7.88e-01 100 seq25_Ideonella_dechlora 5.36e-01 100 seq26_Ideonella_dechlora 7.15e-01 100 seq27_Ideonella_dechlora 5.59e-12 6_[+3(1.24e-08)]_4_[+1(1.17e-07)]_\ 17_[+2(1.40e-05)]_8 seq28_Ideonella_dechlora 9.92e-01 100 seq29_Ideonella_dechlora 7.77e-01 100 seq30_Ideonella_dechlora 2.09e-02 40_[+2(1.89e-05)]_46 seq31_Ideonella_dechlora 7.91e-01 100 seq32_Ideonella_dechlora 1.94e-03 10_[+2(3.23e-06)]_76 seq33_Ideonella_dechlora 4.41e-01 100 seq34_Ideonella_dechlora 9.91e-02 100 seq35_Ideonella_dechlora 8.37e-03 39_[+2(2.19e-05)]_47 seq36_Ideonella_dechlora 8.10e-01 100 seq37_Ideonella_dechlora 3.03e-04 54_[+2(9.96e-08)]_32 seq38_Ideonella_dechlora 3.11e-06 19_[+3(3.47e-10)]_54 seq39_Ideonella_dechlora 3.41e-07 70_[+3(2.02e-10)]_3 seq40_Ideonella_dechlora 9.35e-01 100 seq41_Ideonella_dechlora 5.55e-04 61_[+1(1.96e-07)]_15 seq42_Ideonella_dechlora 2.36e-04 65_[+1(2.09e-07)]_11 seq43_Ideonella_dechlora 4.67e-01 100 seq44_Ideonella_dechlora 6.97e-01 100 seq45_Ideonella_dechlora 4.77e-01 100 seq46_Ideonella_dechlora 2.99e-01 100 seq47_Ideonella_dechlora 8.30e-01 100 seq49_Ideonella_dechlora 5.69e-05 20_[+1(9.75e-05)]_25_[+2(2.66e-06)]_\ 17 seq50_Ideonella_dechlora 6.22e-01 100 seq51_Ideonella_dechlora 6.71e-01 100 seq52_Ideonella_dechlora 5.79e-01 100 seq53_Ideonella_dechlora 7.16e-06 52_[+1(1.10e-09)]_24 seq54_Ideonella_dechlora 3.38e-04 42_[+2(7.33e-06)]_44 seq55_Ideonella_dechlora 1.19e-02 53_[+2(5.15e-06)]_33 seq56_Ideonella_dechlora 2.09e-05 65_[+3(7.58e-09)]_8 seq57_Ideonella_dechlora 8.58e-01 100 seq58_Ideonella_dechlora 8.93e-01 100 seq59_Ideonella_dechlora 2.69e-02 100 seq60_Ideonella_dechlora 3.49e-01 100 seq61_Ideonella_dechlora 5.51e-05 45_[+1(1.24e-08)]_31 seq62_Ideonella_dechlora 3.12e-08 [+1(8.46e-12)]_76 seq63_Ideonella_dechlora 9.74e-01 100 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (3) found. ******************************************************************************** CPU: kodomo ********************************************************************************