******************************************************************************** MEME - Motif discovery tool ******************************************************************************** MEME version 5.5.1 (Release date: Sun Jan 29 10:33:12 2023 -0800) For further information on how to interpret these results please access https://meme-suite.org/meme. To get a copy of the MEME Suite software please access https://meme-suite.org. ******************************************************************************** ******************************************************************************** REFERENCE ******************************************************************************** If you use this program in your research, please cite: Timothy L. Bailey and Charles Elkan, "Fitting a mixture model by expectation maximization to discover motifs in biopolymers", Proceedings of the Second International Conference on Intelligent Systems for Molecular Biology, pp. 28-36, AAAI Press, Menlo Park, California, 1994. ******************************************************************************** ******************************************************************************** TRAINING SET ******************************************************************************** PRIMARY SEQUENCES= train.fa CONTROL SEQUENCES= --none-- ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ seq1_BACSU 1.0000 100 seq2_BACSU 1.0000 100 seq3_BACSU 1.0000 100 seq4_BACSU 1.0000 100 seq5_BACSU 1.0000 100 seq6_BACSU 1.0000 100 seq7_BACSU 1.0000 100 seq8_BACSU 1.0000 100 seq9_BACSU 1.0000 100 seq10_BACSU 1.0000 100 seq11_BACSU 1.0000 100 seq12_BACSU 1.0000 100 seq13_BACSU 1.0000 100 seq14_BACSU 1.0000 100 seq15_BACSU 1.0000 100 seq16_BACSU 1.0000 100 seq17_BACSU 1.0000 100 seq18_BACSU 1.0000 100 seq19_BACSU 1.0000 100 seq20_BACSU 1.0000 100 seq21_BACSU 1.0000 100 seq22_BACSU 1.0000 100 seq23_BACSU 1.0000 100 seq24_BACSU 1.0000 100 seq25_BACSU 1.0000 100 seq26_BACSU 1.0000 100 seq27_BACSU 1.0000 100 seq28_BACSU 1.0000 100 seq29_BACSU 1.0000 100 seq30_BACSU 1.0000 100 seq31_BACSU 1.0000 100 seq32_BACSU 1.0000 100 seq33_BACSU 1.0000 100 seq34_BACSU 1.0000 100 seq35_BACSU 1.0000 100 seq36_BACSU 1.0000 100 seq37_BACSU 1.0000 100 seq38_BACSU 1.0000 100 seq39_BACSU 1.0000 100 seq40_BACSU 1.0000 100 seq41_BACSU 1.0000 100 seq42_BACSU 1.0000 100 seq43_BACSU 1.0000 100 seq44_BACSU 1.0000 100 seq45_BACSU 1.0000 100 seq46_BACSU 1.0000 100 seq47_BACSU 1.0000 100 seq48_BACSU 1.0000 100 seq49_BACSU 1.0000 100 seq50_BACSU 1.0000 100 ******************************************************************************** ******************************************************************************** COMMAND LINE SUMMARY ******************************************************************************** This information can also be useful in the event you wish to report a problem with the MEME software. command: meme train.fa -dna -minw 5 -maxw 50 -nmotifs 3 -text model: mod= zoops nmotifs= 3 evt= inf objective function: em= E-value of product of p-values starts= E-value of product of p-values strands: + width: minw= 5 maxw= 50 nsites: minsites= 2 maxsites= 50 wnsites= 0.8 theta: spmap= uni spfuzz= 0.5 em: prior= dirichlet b= 0.01 maxiter= 50 distance= 1e-05 trim: wg= 11 ws= 1 endgaps= yes data: n= 5000 N= 50 sample: seed= 0 hsfrac= 0 searchsize= 5000 norand= no csites= 1000 Letter frequencies in dataset: A 0.334 C 0.148 G 0.217 T 0.301 Background letter frequencies (from file dataset with add-one prior applied): A 0.334 C 0.148 G 0.217 T 0.301 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF GGKSMKKTTTTTVTTTKSNAWAAADGDDNA MEME-1 width = 30 sites = 18 llr = 253 E-value = 4.0e-011 ******************************************************************************** -------------------------------------------------------------------------------- Motif GGKSMKKTTTTTVTTTKSNAWAAADGDDNA MEME-1 Description -------------------------------------------------------------------------------- Simplified A 21:251:::12241221:384887424329 pos.-specific C 11143:1:1::23:1:24211:1312113: probability G 5744:33:::1:212:352112::25232: matrix T 2141266a9986196841313:1:313331 bits 2.8 2.5 2.2 1.9 Relative 1.7 * Entropy 1.4 *** * (20.2 bits) 1.1 *** * * * * * 0.8 * ***** * * * * *** * 0.6 *********** * * * * *** * 0.3 ****************** * *** * ** 0.0 ------------------------------ Multilevel GGGCATTTTTTTATTTTGTAAAAAAGAACA consensus A TGCGG CC AGCA T CTATGT sequence G C G GTA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGKSMKKTTTTTVTTTKSNAWAAADGDDNA MEME-1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------------------------ seq32_BACSU 60 2.45e-11 CGTTGATTGG TGTCCGTTTTTTATTTGCCAAAAATGAGGA GGATCATAGA seq28_BACSU 35 1.35e-10 AAAGAAGCAT GGTCAGTTTTTAATTTGGGATAAAGGTTCA GCCGTATCCC seq44_BACSU 56 1.97e-09 ATGGGATGAG AGGGCTTTTTTTATTTTCTGAAAAAATGCA GTGGAGGAAT seq37_BACSU 52 4.12e-09 TATGGGGATG AGGGCTCTTTTTATTTTCGATAAATCAATA AAAAAAGGAG seq24_BACSU 15 5.21e-09 GTGGTAAACA GGGGATTTTTACATATCGCAAAAATAATCA AAACATATAA seq41_BACSU 31 3.58e-08 AAGCGCCATT TGCTCTTTTTTTGTGTTCTATAACAGAGAA AGACGCCATT seq25_BACSU 50 1.20e-07 TCGAATAGAG CAGACGGTTTTTATTTTCCACAAAAATAAA ACCAAAGGAG seq49_BACSU 9 1.43e-07 TAATATTA GGTGAGTTTTTTGTTATGTAAAAAGAGCTT TTGGAATCGA seq5_BACSU 59 1.43e-07 GGCTTGAATA GGCCAAGTTTTTCTTTCGCTTAAAACTAGA GGTGATTATA seq43_BACSU 35 2.38e-07 CTTGTCTAAA GGGCAGTTTTATAAGTGGTAAATCACGACA TTACTGAAAC seq15_BACSU 32 2.81e-07 GTCTTGTAAA AGTATTTTCTTTCTTTGGAAGAAATGCTTA TTACACATAT seq48_BACSU 67 3.87e-07 ATTGGGATGG GCTCTTTTTTGTGTTTGTAAAAAAGGAGGA AAAA seq22_BACSU 44 4.52e-07 CCTGTAAACG GCTGCTTTCTTCATTATGTATGAACTTACA TTTTTTAACG seq21_BACSU 40 4.52e-07 ATGGCAAGGT GTTCAGGTTTTTCTCACGGAGAACTGTCTA ACGTGATGTA seq36_BACSU 1 6.13e-07 . AAGGATGTTTACCGATGCAAAAAAAGGGCA AAATGGATAG seq34_BACSU 57 2.16e-06 CTAATTCCAG CGGCATGTTATACTGAACAAAAACGGAAAA AAGGGTGGAT seq6_BACSU 11 2.16e-06 TTCAAATTAT TGTATTGTTTTCGTATTCAATGTCAGATAA AATATTCTTA seq14_BACSU 36 4.55e-06 ATAACGGCAG GGGGATTTTTTATTTTTGTCCGCCTTGTTA TGATGAGAGA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGKSMKKTTTTTVTTTKSNAWAAADGDDNA MEME-1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- seq32_BACSU 2.5e-11 59_[+1]_11 seq28_BACSU 1.3e-10 34_[+1]_36 seq44_BACSU 2e-09 55_[+1]_15 seq37_BACSU 4.1e-09 51_[+1]_19 seq24_BACSU 5.2e-09 14_[+1]_56 seq41_BACSU 3.6e-08 30_[+1]_40 seq25_BACSU 1.2e-07 49_[+1]_21 seq49_BACSU 1.4e-07 8_[+1]_62 seq5_BACSU 1.4e-07 58_[+1]_12 seq43_BACSU 2.4e-07 34_[+1]_36 seq15_BACSU 2.8e-07 31_[+1]_39 seq48_BACSU 3.9e-07 66_[+1]_4 seq22_BACSU 4.5e-07 43_[+1]_27 seq21_BACSU 4.5e-07 39_[+1]_31 seq36_BACSU 6.1e-07 [+1]_70 seq34_BACSU 2.2e-06 56_[+1]_14 seq6_BACSU 2.2e-06 10_[+1]_60 seq14_BACSU 4.5e-06 35_[+1]_35 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGKSMKKTTTTTVTTTKSNAWAAADGDDNA MEME-1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF GGKSMKKTTTTTVTTTKSNAWAAADGDDNA width=30 seqs=18 seq32_BACSU ( 60) TGTCCGTTTTTTATTTGCCAAAAATGAGGA 1 seq28_BACSU ( 35) GGTCAGTTTTTAATTTGGGATAAAGGTTCA 1 seq44_BACSU ( 56) AGGGCTTTTTTTATTTTCTGAAAAAATGCA 1 seq37_BACSU ( 52) AGGGCTCTTTTTATTTTCGATAAATCAATA 1 seq24_BACSU ( 15) GGGGATTTTTACATATCGCAAAAATAATCA 1 seq41_BACSU ( 31) TGCTCTTTTTTTGTGTTCTATAACAGAGAA 1 seq25_BACSU ( 50) CAGACGGTTTTTATTTTCCACAAAAATAAA 1 seq49_BACSU ( 9) GGTGAGTTTTTTGTTATGTAAAAAGAGCTT 1 seq5_BACSU ( 59) GGCCAAGTTTTTCTTTCGCTTAAAACTAGA 1 seq43_BACSU ( 35) GGGCAGTTTTATAAGTGGTAAATCACGACA 1 seq15_BACSU ( 32) AGTATTTTCTTTCTTTGGAAGAAATGCTTA 1 seq48_BACSU ( 67) GCTCTTTTTTGTGTTTGTAAAAAAGGAGGA 1 seq22_BACSU ( 44) GCTGCTTTCTTCATTATGTATGAACTTACA 1 seq21_BACSU ( 40) GTTCAGGTTTTTCTCACGGAGAACTGTCTA 1 seq36_BACSU ( 1) AAGGATGTTTACCGATGCAAAAAAAGGGCA 1 seq34_BACSU ( 57) CGGCATGTTATACTGAACAAAAACGGAAAA 1 seq6_BACSU ( 11) TGTATTGTTTTCGTATTCAATGTCAGATAA 1 seq14_BACSU ( 36) GGGGATTTTTTATTTTTGTCCGCCTTGTTA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGKSMKKTTTTTVTTTKSNAWAAADGDDNA MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 30 n= 3550 bayes= 7.7513 E= 4.0e-011 -59 -42 121 -85 -159 -42 174 -243 -1081 -42 104 56 -100 139 84 -243 58 117 -1081 -85 -258 -1081 62 102 -1081 -142 62 102 -1081 -1081 -1081 173 -1081 -42 -1081 156 -258 -1081 -1081 165 -100 -1081 -196 137 -100 58 -1081 102 41 90 4 -243 -258 -1081 -196 156 -100 -142 -38 102 -59 -1081 -1081 137 -258 17 62 56 -1081 158 121 -243 -26 58 -38 15 132 -142 -196 -243 41 -42 -96 15 132 -1081 -38 -1081 132 -142 -1081 -144 100 117 -1081 -1081 22 -142 4 15 -59 17 121 -144 22 -142 4 15 0 -42 36 -12 -59 117 -38 -12 150 -1081 -1081 -243 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGKSMKKTTTTTVTTTKSNAWAAADGDDNA MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 30 nsites= 18 E= 4.0e-011 0.222222 0.111111 0.500000 0.166667 0.111111 0.111111 0.722222 0.055556 0.000000 0.111111 0.444444 0.444444 0.166667 0.388889 0.388889 0.055556 0.500000 0.333333 0.000000 0.166667 0.055556 0.000000 0.333333 0.611111 0.000000 0.055556 0.333333 0.611111 0.000000 0.000000 0.000000 1.000000 0.000000 0.111111 0.000000 0.888889 0.055556 0.000000 0.000000 0.944444 0.166667 0.000000 0.055556 0.777778 0.166667 0.222222 0.000000 0.611111 0.444444 0.277778 0.222222 0.055556 0.055556 0.000000 0.055556 0.888889 0.166667 0.055556 0.166667 0.611111 0.222222 0.000000 0.000000 0.777778 0.055556 0.166667 0.333333 0.444444 0.000000 0.444444 0.500000 0.055556 0.277778 0.222222 0.166667 0.333333 0.833333 0.055556 0.055556 0.055556 0.444444 0.111111 0.111111 0.333333 0.833333 0.000000 0.166667 0.000000 0.833333 0.055556 0.000000 0.111111 0.666667 0.333333 0.000000 0.000000 0.388889 0.055556 0.222222 0.333333 0.222222 0.166667 0.500000 0.111111 0.388889 0.055556 0.222222 0.333333 0.333333 0.111111 0.277778 0.277778 0.222222 0.333333 0.166667 0.277778 0.944444 0.000000 0.000000 0.055556 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGKSMKKTTTTTVTTTKSNAWAAADGDDNA MEME-1 regular expression -------------------------------------------------------------------------------- [GA]G[GT][CG][AC][TG][TG]TTTT[TC][ACG]TT[TA][TG][GC][TAC]A[AT]AA[AC][ATG][GA][ATG][AGT][CTA]A -------------------------------------------------------------------------------- Time 2.52 secs. ******************************************************************************** ******************************************************************************** MOTIF AAAAGGAGG MEME-2 width = 9 sites = 17 llr = 154 E-value = 9.8e-005 ******************************************************************************** -------------------------------------------------------------------------------- Motif AAAAGGAGG MEME-2 Description -------------------------------------------------------------------------------- Simplified A 9999::7:: pos.-specific C 111::1::1 probability G :::1a9389 matrix T :::::::21 bits 2.8 2.5 2.2 * 1.9 ** Relative 1.7 ** * Entropy 1.4 * * ** ** (13.0 bits) 1.1 ****** ** 0.8 ********* 0.6 ********* 0.3 ********* 0.0 --------- Multilevel AAAAGGAGG consensus G sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAAAGGAGG MEME-2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------- seq41_BACSU 78 9.22e-06 ATTTTCTAAG AAAAGGAGG GACGTGCCGG seq21_BACSU 84 9.22e-06 GATGTAGGCG AAAAGGAGG GAAAATAA seq19_BACSU 82 9.22e-06 ATCCGACTTA AAAAGGAGG ATGATTCAAA seq10_BACSU 84 9.22e-06 ATATAATAAA AAAAGGAGG GGCCTATT seq3_BACSU 89 1.52e-05 TAATGTGTAA AAAAGGGGG GCA seq46_BACSU 22 1.93e-05 CAAAAATTTA ACAAGGAGG ACGAGAGAAT seq13_BACSU 81 1.93e-05 TCAACAGATC ACAAGGAGG ACGTTATCTT seq39_BACSU 82 2.53e-05 ATTTCGATTT AAAGGGAGG CTATGTGACT seq18_BACSU 84 4.07e-05 TTAGTAAAGG AAAAGGATG TGGCATCA seq12_BACSU 85 4.07e-05 AATTGAGTGA AAAAGGATG CGTATCA seq25_BACSU 82 4.89e-05 AAAATAAAAC CAAAGGAGG AGTCACATTA seq9_BACSU 83 5.28e-05 GCTGACTGGT AAAGGGGGG CGTTCAAGA seq44_BACSU 8 7.37e-05 TTTTTCT AAAAGGGTG GTACCGCGAG seq17_BACSU 80 7.37e-05 CGTATATTCA AAAAGGAGC CCTTTATTGC seq1_BACSU 84 7.90e-05 ACCGGTACAA AACAGGGGG AGAAGGCA seq26_BACSU 65 8.71e-05 CAGTCTAAAG AAAAGCGGG GCGCGAAAGA seq37_BACSU 84 1.03e-04 AATCAATAAA AAAAGGAGT GTTTCGCA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAAAGGAGG MEME-2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- seq41_BACSU 9.2e-06 77_[+2]_14 seq21_BACSU 9.2e-06 83_[+2]_8 seq19_BACSU 9.2e-06 81_[+2]_10 seq10_BACSU 9.2e-06 83_[+2]_8 seq3_BACSU 1.5e-05 88_[+2]_3 seq46_BACSU 1.9e-05 21_[+2]_70 seq13_BACSU 1.9e-05 80_[+2]_11 seq39_BACSU 2.5e-05 81_[+2]_10 seq18_BACSU 4.1e-05 83_[+2]_8 seq12_BACSU 4.1e-05 84_[+2]_7 seq25_BACSU 4.9e-05 81_[+2]_10 seq9_BACSU 5.3e-05 82_[+2]_9 seq44_BACSU 7.4e-05 7_[+2]_84 seq17_BACSU 7.4e-05 79_[+2]_12 seq1_BACSU 7.9e-05 83_[+2]_8 seq26_BACSU 8.7e-05 64_[+2]_27 seq37_BACSU 0.0001 83_[+2]_8 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAAAGGAGG MEME-2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF AAAAGGAGG width=9 seqs=17 seq41_BACSU ( 78) AAAAGGAGG 1 seq21_BACSU ( 84) AAAAGGAGG 1 seq19_BACSU ( 82) AAAAGGAGG 1 seq10_BACSU ( 84) AAAAGGAGG 1 seq3_BACSU ( 89) AAAAGGGGG 1 seq46_BACSU ( 22) ACAAGGAGG 1 seq13_BACSU ( 81) ACAAGGAGG 1 seq39_BACSU ( 82) AAAGGGAGG 1 seq18_BACSU ( 84) AAAAGGATG 1 seq12_BACSU ( 85) AAAAGGATG 1 seq25_BACSU ( 82) CAAAGGAGG 1 seq9_BACSU ( 83) AAAGGGGGG 1 seq44_BACSU ( 8) AAAAGGGTG 1 seq17_BACSU ( 80) AAAAGGAGC 1 seq1_BACSU ( 84) AACAGGGGG 1 seq26_BACSU ( 65) AAAAGCGGG 1 seq37_BACSU ( 84) AAAAGGAGT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAAAGGAGG MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 9 n= 4600 bayes= 8.87156 E= 9.8e-005 150 -133 -1073 -1073 140 -34 -1073 -1073 150 -133 -1073 -1073 140 -1073 -88 -1073 -1073 -1073 221 -1073 -1073 -133 212 -1073 108 -1073 44 -1073 -1073 -1073 193 -77 -1073 -133 203 -235 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAAAGGAGG MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 9 nsites= 17 E= 9.8e-005 0.941176 0.058824 0.000000 0.000000 0.882353 0.117647 0.000000 0.000000 0.941176 0.058824 0.000000 0.000000 0.882353 0.000000 0.117647 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.058824 0.941176 0.000000 0.705882 0.000000 0.294118 0.000000 0.000000 0.000000 0.823529 0.176471 0.000000 0.058824 0.882353 0.058824 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAAAGGAGG MEME-2 regular expression -------------------------------------------------------------------------------- AAAAGG[AG]GG -------------------------------------------------------------------------------- Time 4.60 secs. ******************************************************************************** ******************************************************************************** MOTIF YAYWDMMGNHCTCDKCCHTTWKTSKRDRRB MEME-3 width = 30 sites = 13 llr = 200 E-value = 1.8e-004 ******************************************************************************** -------------------------------------------------------------------------------- Motif YAYWDMMGNHCTCDKCCHTTWKTSKRDRRB MEME-3 Description -------------------------------------------------------------------------------- Simplified A :72544322412:2:::2::41::25343: pos.-specific C 5142:35:32628119a31::::3211::5 probability G 121142262:122431:1::1335352552 matrix T 5:4322123425:36::49a56724:4123 bits 2.8 * 2.5 * 2.2 ** 1.9 * ** Relative 1.7 * ** * Entropy 1.4 * ** ** (22.2 bits) 1.1 * ** ** * 0.8 * * * *** ** ** * 0.6 ** ** * * *** ****** * *** 0.3 *** ********* ********** * *** 0.0 ------------------------------ Multilevel CACAAACGCACTCGTCCTTTTTTGTATGGC consensus TGTTGCAATTTCGTG C AGGCGGAAAT sequence T GC A A G G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif YAYWDMMGNHCTCDKCCHTTWKTSKRDRRB MEME-3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------------------------ seq40_BACSU 40 1.19e-11 GATTTGCACT TATCGCCGCTCTCGTCCTTTGGGCGGGAGC TTTTTGACAT seq1_BACSU 5 1.14e-10 ATTG CAGCGCCGGTCGCTCCCTTTATTGTATGGC CGCGGTCAGA seq21_BACSU 5 2.47e-09 AGGT TGCTGACACACCCGGCCGCTTTGCCATGGC AAGGTGTTCA seq44_BACSU 26 8.56e-09 GGTACCGCGA GATAAGCTTTCTCGTCCCTTATGGGATGAG AGGGCTTTTT seq37_BACSU 22 1.45e-08 AGGGTGGCAA CGCGAGAGCTCTCGTCCCTTTATGGGGATG AGGGCTCTTT seq26_BACSU 19 1.60e-08 TAATGTAACA TATTATCGTACTGTGCCCTTAGTGTACAAC AAAAAACAGT seq23_BACSU 39 2.89e-08 GAATTTTTCT TATTGAAGATCCGTGCCATTTGTCAGTAGC GTTCTTTTTG seq48_BACSU 37 1.02e-07 TGGTACCGCG TGCATTGAGCCACGTCCCTTATTGGGATGG GCTCTTTTTT seq3_BACSU 31 1.20e-07 GAGAGATTGT CACTAAAGTCTCCAGCCATTTGGTTGGGTT AGGAACCAGC seq39_BACSU 17 2.09e-07 GTCTGTTTTA CAAAGCGGTATGCTTGCTTTTTTGAATGGT GAATGATACA seq24_BACSU 48 3.77e-07 ATAATCAAAA CATATAATCCGTGATCCATTATTCTAAAAC AGAAAGGAGA seq47_BACSU 14 4.05e-07 TTGAACTGAT CCAAACCGAATTCCTCCTTTTTTTTCAGAT CAGCTGTATT seq27_BACSU 64 4.98e-07 TAGGGATCTA TACATATAGAAACATCCTTTTTTGCGAGGT GCTCCCA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif YAYWDMMGNHCTCDKCCHTTWKTSKRDRRB MEME-3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- seq40_BACSU 1.2e-11 39_[+3]_31 seq1_BACSU 1.1e-10 4_[+3]_66 seq21_BACSU 2.5e-09 4_[+3]_66 seq44_BACSU 8.6e-09 25_[+3]_45 seq37_BACSU 1.4e-08 21_[+3]_49 seq26_BACSU 1.6e-08 18_[+3]_52 seq23_BACSU 2.9e-08 38_[+3]_32 seq48_BACSU 1e-07 36_[+3]_34 seq3_BACSU 1.2e-07 30_[+3]_40 seq39_BACSU 2.1e-07 16_[+3]_54 seq24_BACSU 3.8e-07 47_[+3]_23 seq47_BACSU 4e-07 13_[+3]_57 seq27_BACSU 5e-07 63_[+3]_7 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif YAYWDMMGNHCTCDKCCHTTWKTSKRDRRB MEME-3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF YAYWDMMGNHCTCDKCCHTTWKTSKRDRRB width=30 seqs=13 seq40_BACSU ( 40) TATCGCCGCTCTCGTCCTTTGGGCGGGAGC 1 seq1_BACSU ( 5) CAGCGCCGGTCGCTCCCTTTATTGTATGGC 1 seq21_BACSU ( 5) TGCTGACACACCCGGCCGCTTTGCCATGGC 1 seq44_BACSU ( 26) GATAAGCTTTCTCGTCCCTTATGGGATGAG 1 seq37_BACSU ( 22) CGCGAGAGCTCTCGTCCCTTTATGGGGATG 1 seq26_BACSU ( 19) TATTATCGTACTGTGCCCTTAGTGTACAAC 1 seq23_BACSU ( 39) TATTGAAGATCCGTGCCATTTGTCAGTAGC 1 seq48_BACSU ( 37) TGCATTGAGCCACGTCCCTTATTGGGATGG 1 seq3_BACSU ( 31) CACTAAAGTCTCCAGCCATTTGGTTGGGTT 1 seq39_BACSU ( 17) CAAAGCGGTATGCTTGCTTTTTTGAATGGT 1 seq24_BACSU ( 48) CATATAATCCGTGATCCATTATTCTAAAAC 1 seq47_BACSU ( 14) CCAAACCGAATTCCTCCTTTTTTTTCAGAT 1 seq27_BACSU ( 64) TACATATAGAAACATCCTTTTTTGCGAGGT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif YAYWDMMGNHCTCDKCCHTTWKTSKRDRRB MEME-3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 30 n= 3550 bayes= 6.96447 E= 1.8e-004 -1035 164 -149 62 105 -95 9 -1035 -112 137 -149 35 47 5 -149 3 20 -1035 83 -38 20 105 -49 -97 -12 164 -49 -197 -53 -1035 151 -97 -112 105 9 3 20 64 -1035 35 -211 205 -149 -38 -112 64 -49 62 -1035 237 9 -1035 -53 -95 83 3 -1035 -95 51 103 -1035 264 -149 -1035 -1035 275 -1035 -1035 -53 105 -149 35 -1035 -95 -1035 162 -1035 -1035 -1035 173 20 -1035 -149 84 -211 -1035 51 103 -1035 -1035 51 120 -1035 105 131 -97 -112 5 51 35 47 -95 109 -1035 -12 -95 9 35 20 -1035 131 -197 -12 -1035 131 -97 -1035 164 9 3 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif YAYWDMMGNHCTCDKCCHTTWKTSKRDRRB MEME-3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 30 nsites= 13 E= 1.8e-004 0.000000 0.461538 0.076923 0.461538 0.692308 0.076923 0.230769 0.000000 0.153846 0.384615 0.076923 0.384615 0.461538 0.153846 0.076923 0.307692 0.384615 0.000000 0.384615 0.230769 0.384615 0.307692 0.153846 0.153846 0.307692 0.461538 0.153846 0.076923 0.230769 0.000000 0.615385 0.153846 0.153846 0.307692 0.230769 0.307692 0.384615 0.230769 0.000000 0.384615 0.076923 0.615385 0.076923 0.230769 0.153846 0.230769 0.153846 0.461538 0.000000 0.769231 0.230769 0.000000 0.230769 0.076923 0.384615 0.307692 0.000000 0.076923 0.307692 0.615385 0.000000 0.923077 0.076923 0.000000 0.000000 1.000000 0.000000 0.000000 0.230769 0.307692 0.076923 0.384615 0.000000 0.076923 0.000000 0.923077 0.000000 0.000000 0.000000 1.000000 0.384615 0.000000 0.076923 0.538462 0.076923 0.000000 0.307692 0.615385 0.000000 0.000000 0.307692 0.692308 0.000000 0.307692 0.538462 0.153846 0.153846 0.153846 0.307692 0.384615 0.461538 0.076923 0.461538 0.000000 0.307692 0.076923 0.230769 0.384615 0.384615 0.000000 0.538462 0.076923 0.307692 0.000000 0.538462 0.153846 0.000000 0.461538 0.230769 0.307692 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif YAYWDMMGNHCTCDKCCHTTWKTSKRDRRB MEME-3 regular expression -------------------------------------------------------------------------------- [CT][AG][CT][AT][AGT][AC][CA][GA][CTG][ATC][CT][TC][CG][GTA][TG]CC[TCA]TT[TA][TG][TG][GC][TG][AG][TAG][GA][GA][CTG] -------------------------------------------------------------------------------- Time 6.70 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- seq1_BACSU 2.92e-09 4_[+3(1.14e-10)]_49_[+2(7.90e-05)]_\ 8 seq2_BACSU 9.55e-01 100 seq3_BACSU 1.10e-06 30_[+3(1.20e-07)]_28_[+2(1.52e-05)]_\ 3 seq4_BACSU 7.64e-01 100 seq5_BACSU 2.28e-04 58_[+1(1.43e-07)]_12 seq6_BACSU 2.47e-03 10_[+1(2.16e-06)]_60 seq7_BACSU 2.20e-01 100 seq8_BACSU 6.27e-01 100 seq9_BACSU 3.03e-02 82_[+2(5.28e-05)]_9 seq10_BACSU 9.47e-03 83_[+2(9.22e-06)]_8 seq11_BACSU 8.22e-01 100 seq12_BACSU 5.96e-03 84_[+2(4.07e-05)]_7 seq13_BACSU 1.40e-02 80_[+2(1.93e-05)]_11 seq14_BACSU 4.16e-04 35_[+1(4.55e-06)]_35 seq15_BACSU 3.32e-04 31_[+1(2.81e-07)]_39 seq16_BACSU 8.25e-01 100 seq17_BACSU 8.45e-02 79_[+2(7.37e-05)]_12 seq18_BACSU 4.67e-02 83_[+2(4.07e-05)]_8 seq19_BACSU 2.10e-02 81_[+2(9.22e-06)]_10 seq20_BACSU 5.03e-01 100 seq21_BACSU 2.75e-12 4_[+3(2.47e-09)]_5_[+1(4.52e-07)]_\ 14_[+2(9.22e-06)]_8 seq22_BACSU 1.54e-04 43_[+1(4.52e-07)]_27 seq23_BACSU 3.63e-05 38_[+3(2.89e-08)]_32 seq24_BACSU 7.16e-10 14_[+1(5.21e-09)]_3_[+3(3.77e-07)]_\ 23 seq25_BACSU 5.78e-06 49_[+1(1.20e-07)]_2_[+2(4.89e-05)]_\ 10 seq26_BACSU 8.87e-07 18_[+3(1.60e-08)]_16_[+2(8.71e-05)]_\ 27 seq27_BACSU 2.01e-03 63_[+3(4.98e-07)]_7 seq28_BACSU 2.01e-07 34_[+1(1.35e-10)]_36 seq29_BACSU 3.51e-01 100 seq30_BACSU 6.11e-02 100 seq31_BACSU 3.59e-01 100 seq32_BACSU 4.18e-09 59_[+1(2.45e-11)]_11 seq33_BACSU 4.26e-01 100 seq34_BACSU 7.71e-05 56_[+1(2.16e-06)]_14 seq35_BACSU 4.49e-01 100 seq36_BACSU 3.98e-04 [+1(6.13e-07)]_70 seq37_BACSU 1.68e-12 21_[+3(1.45e-08)]_[+1(4.12e-09)]_19 seq38_BACSU 2.81e-01 100 seq39_BACSU 1.42e-06 16_[+3(2.09e-07)]_35_[+2(2.53e-05)]_\ 10 seq40_BACSU 5.19e-08 39_[+3(1.19e-11)]_31 seq41_BACSU 2.30e-08 30_[+1(3.58e-08)]_17_[+2(9.22e-06)]_\ 14 seq42_BACSU 2.27e-01 100 seq43_BACSU 4.29e-06 34_[+1(2.38e-07)]_36 seq44_BACSU 3.75e-13 7_[+2(7.37e-05)]_9_[+3(8.56e-09)]_\ [+1(1.97e-09)]_15 seq45_BACSU 2.75e-02 100 seq46_BACSU 1.47e-02 21_[+2(1.93e-05)]_70 seq47_BACSU 2.63e-04 13_[+3(4.05e-07)]_57 seq48_BACSU 7.77e-11 36_[+3(1.02e-07)]_[+1(3.87e-07)]_4 seq49_BACSU 1.19e-04 8_[+1(1.43e-07)]_62 seq50_BACSU 6.81e-01 100 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (3) found. ******************************************************************************** CPU: kodomo ********************************************************************************