******************************************************************************** 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 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 0.264 C 0.22 G 0.239 T 0.277 Background letter frequencies (from file dataset with add-one prior applied): A 0.264 C 0.22 G 0.239 T 0.277 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF RCCBTTDTGCTAHAVTVCSCACCCYTTT MEME-1 width = 28 sites = 9 llr = 172 E-value = 1.0e-007 ******************************************************************************** -------------------------------------------------------------------------------- Motif RCCBTTDTGCTAHAVTVCSCACCCYTTT MEME-1 Description -------------------------------------------------------------------------------- Simplified A 3:1:2:311::9294:21:16::11::: pos.-specific C 18731:11:9::2:21363729974::: probability G 6122:12191:11:2:426221::111: matrix T :1:47937::a:4119:11:::12399a bits 2.2 2.0 1.7 ** ** * 1.5 **** ** * Relative 1.3 * **** * * ** *** Entropy 1.1 * * **** * * ** *** (27.6 bits) 0.9 ** * **** * * * *** *** 0.7 *** ** **** * * ****** *** 0.4 ****** ***** * ********* *** 0.2 ****** ********************* 0.0 ---------------------------- Multilevel GCCTTTATGCTATAATGCGCACCCCTTT consensus A GCA T A C CGCGC TT sequence G G C G A G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RCCBTTDTGCTAHAVTVCSCACCCYTTT MEME-1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------------------- seq45_BACSU 53 2.80e-13 ACGCGCCGGG GCGTTTGTGCTAAACTGCGCACCCTTTT TTTCTGTGGT seq39_BACSU 48 1.07e-10 ACAGCCACTC GCCCTTATGCTGCAATCTGCCCCCCTGT AATCGCGATC seq47_BACSU 51 1.30e-10 ATCTCGGCTC CGCTTTCTGCTACAATCCCCACCCCGTT CGAAGATTGA seq42_BACSU 48 2.54e-10 CCTGTGGTGT ATCTTTATGCTATAGTAGCGCCCCTTTT TACCCGGATG seq7_BACSU 51 7.97e-10 GACATAGGGC ACATATTGGCTATAATGCGCACCAATTT TCTTTAAGTA seq27_BACSU 59 2.24e-09 ATAGAAAGAA GCCGTTAAGCTATAGCGATGACCCTTTT GCAGGAGAGC seq10_BACSU 46 3.02e-09 CGCACCCACA GCCCTTTTGGTAATATCGGAAGCCCTTT TTACAACAGA seq33_BACSU 55 4.34e-09 CGCAGATACG ACGGATTTGCTATATTGCGCGCTTGTTT AACAGGAGTG seq13_BACSU 52 1.94e-08 CAGCCAGACC GCCCCGGCACTAGACTACCCGCCTCTTT ATTCAGTCTG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RCCBTTDTGCTAHAVTVCSCACCCYTTT MEME-1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- seq45_BACSU 2.8e-13 52_[+1]_20 seq39_BACSU 1.1e-10 47_[+1]_25 seq47_BACSU 1.3e-10 50_[+1]_22 seq42_BACSU 2.5e-10 47_[+1]_25 seq7_BACSU 8e-10 50_[+1]_22 seq27_BACSU 2.2e-09 58_[+1]_14 seq10_BACSU 3e-09 45_[+1]_27 seq33_BACSU 4.3e-09 54_[+1]_18 seq13_BACSU 1.9e-08 51_[+1]_21 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RCCBTTDTGCTAHAVTVCSCACCCYTTT MEME-1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF RCCBTTDTGCTAHAVTVCSCACCCYTTT width=28 seqs=9 seq45_BACSU ( 53) GCGTTTGTGCTAAACTGCGCACCCTTTT 1 seq39_BACSU ( 48) GCCCTTATGCTGCAATCTGCCCCCCTGT 1 seq47_BACSU ( 51) CGCTTTCTGCTACAATCCCCACCCCGTT 1 seq42_BACSU ( 48) ATCTTTATGCTATAGTAGCGCCCCTTTT 1 seq7_BACSU ( 51) ACATATTGGCTATAATGCGCACCAATTT 1 seq27_BACSU ( 59) GCCGTTAAGCTATAGCGATGACCCTTTT 1 seq10_BACSU ( 46) GCCCTTTTGGTAATATCGGAAGCCCTTT 1 seq33_BACSU ( 55) ACGGATTTGCTATATTGCGCGCTTGTTT 1 seq13_BACSU ( 52) GCCCCGGCACTAGACTACCCGCCTCTTT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RCCBTTDTGCTAHAVTVCSCACCCYTTT MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 28 n= 3650 bayes= 7.96 E= 1.0e-007 34 -98 121 -982 -982 182 -110 -132 -125 160 -11 -982 -982 60 -11 68 -25 -98 -982 126 -982 -982 -110 168 34 -98 -11 26 -125 -98 -110 126 -125 -982 189 -982 -982 202 -110 -982 -982 -982 -982 185 175 -982 -110 -982 -25 2 -110 68 175 -982 -982 -132 75 2 -11 -132 -982 -98 -982 168 -25 60 89 -982 -125 134 -11 -132 -982 60 121 -132 -125 160 -11 -982 107 2 -11 -982 -982 202 -110 -982 -982 202 -982 -132 -125 160 -982 -32 -125 102 -110 26 -982 -982 -110 168 -982 -982 -110 168 -982 -982 -982 185 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RCCBTTDTGCTAHAVTVCSCACCCYTTT MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 28 nsites= 9 E= 1.0e-007 0.333333 0.111111 0.555556 0.000000 0.000000 0.777778 0.111111 0.111111 0.111111 0.666667 0.222222 0.000000 0.000000 0.333333 0.222222 0.444444 0.222222 0.111111 0.000000 0.666667 0.000000 0.000000 0.111111 0.888889 0.333333 0.111111 0.222222 0.333333 0.111111 0.111111 0.111111 0.666667 0.111111 0.000000 0.888889 0.000000 0.000000 0.888889 0.111111 0.000000 0.000000 0.000000 0.000000 1.000000 0.888889 0.000000 0.111111 0.000000 0.222222 0.222222 0.111111 0.444444 0.888889 0.000000 0.000000 0.111111 0.444444 0.222222 0.222222 0.111111 0.000000 0.111111 0.000000 0.888889 0.222222 0.333333 0.444444 0.000000 0.111111 0.555556 0.222222 0.111111 0.000000 0.333333 0.555556 0.111111 0.111111 0.666667 0.222222 0.000000 0.555556 0.222222 0.222222 0.000000 0.000000 0.888889 0.111111 0.000000 0.000000 0.888889 0.000000 0.111111 0.111111 0.666667 0.000000 0.222222 0.111111 0.444444 0.111111 0.333333 0.000000 0.000000 0.111111 0.888889 0.000000 0.000000 0.111111 0.888889 0.000000 0.000000 0.000000 1.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RCCBTTDTGCTAHAVTVCSCACCCYTTT MEME-1 regular expression -------------------------------------------------------------------------------- [GA]C[CG][TCG][TA]T[ATG]TGCTA[TAC]A[ACG]T[GCA][CG][GC][CG][ACG]CC[CT][CT]TTT -------------------------------------------------------------------------------- Time 2.77 secs. ******************************************************************************** ******************************************************************************** MOTIF TKCKBGSBCVHCTHTTSHMCGCCSGHTGGHMADCCCGTC MEME-2 width = 39 sites = 4 llr = 130 E-value = 2.5e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif TKCKBGSBCVHCTHTTSHMCGCCSGHTGGHMADCCCGTC MEME-2 Description -------------------------------------------------------------------------------- Simplified A :::::::::53333:::35::::::3:3:35a33::::: pos.-specific C ::a:5:53a358:33:555838a5:3:::55::888::8 probability G :5:53853:3::::::5::38::5a:38a:::5:3383: matrix T a5:533:5::3:858a:3:::3:::58::3::3:::383 bits 2.2 * * * 2.0 * * * * * * 1.7 * * * * * * * * 1.5 * * * * * * * * Relative 1.3 * * * * * **** * ** * *** * Entropy 1.1 * * ** * ** *** ******* *** ** ****** (46.8 bits) 0.9 **** ** * ** *** ******* *** ** ****** 0.7 ******* * ** *** ******* *** ** ****** 0.4 *************************************** 0.2 *************************************** 0.0 --------------------------------------- Multilevel TGCGCGCTCACCTTTTCCACGCCCGTTGGCAAGCCCGTC consensus T TGTGC CAAAAC GACGCT G AGA AC AAGGTGT sequence T G GT C T C T T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TKCKBGSBCVHCTHTTSHMCGCCSGHTGGHMADCCCGTC MEME-2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------------------------- seq8_BACSU 22 5.97e-18 ACAGAAATAA TGCGCGCTCGCCTCCTCCCCGTCGGTTGGCAAGCCCGGC CAATTCCATT seq29_BACSU 7 1.20e-15 TCATCC TGCTGGCCCATCTTTTCTCCCCCCGCTGGACAGCGGGTC ACGCACTGAT seq36_BACSU 43 5.63e-15 AAACAAATGT TTCTTTGGCCCCTTTTGCACGCCCGTGGGTAATACCGTT TCAATCAGGC seq28_BACSU 11 1.16e-14 ATTTACGAAT TTCGCGGTCAAAAATTGAAGGCCGGATAGCCAACCCTTC ATTACTATCA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TKCKBGSBCVHCTHTTSHMCGCCSGHTGGHMADCCCGTC MEME-2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- seq8_BACSU 6e-18 21_[+2]_40 seq29_BACSU 1.2e-15 6_[+2]_55 seq36_BACSU 5.6e-15 42_[+2]_19 seq28_BACSU 1.2e-14 10_[+2]_51 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TKCKBGSBCVHCTHTTSHMCGCCSGHTGGHMADCCCGTC MEME-2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF TKCKBGSBCVHCTHTTSHMCGCCSGHTGGHMADCCCGTC width=39 seqs=4 seq8_BACSU ( 22) TGCGCGCTCGCCTCCTCCCCGTCGGTTGGCAAGCCCGGC 1 seq29_BACSU ( 7) TGCTGGCCCATCTTTTCTCCCCCCGCTGGACAGCGGGTC 1 seq36_BACSU ( 43) TTCTTTGGCCCCTTTTGCACGCCCGTGGGTAATACCGTT 1 seq28_BACSU ( 11) TTCGCGGTCAAAAATTGAAGGCCGGATAGCCAACCCTTC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TKCKBGSBCVHCTHTTSHMCGCCSGHTGGHMADCCCGTC MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 39 n= 3100 bayes= 10.3339 E= 2.5e+001 -865 -865 -865 185 -865 -865 106 85 -865 218 -865 -865 -865 -865 106 85 -865 118 6 -15 -865 -865 165 -15 -865 118 106 -865 -865 19 6 85 -865 218 -865 -865 92 19 6 -865 -8 118 -865 -15 -8 177 -865 -865 -8 -865 -865 143 -8 19 -865 85 -865 19 -865 143 -865 -865 -865 185 -865 118 106 -865 -8 118 -865 -15 92 118 -865 -865 -865 177 6 -865 -865 19 165 -865 -865 177 -865 -15 -865 218 -865 -865 -865 118 106 -865 -865 -865 206 -865 -8 19 -865 85 -865 -865 6 143 -8 -865 165 -865 -865 -865 206 -865 -8 118 -865 -15 92 118 -865 -865 192 -865 -865 -865 -8 -865 106 -15 -8 177 -865 -865 -865 177 6 -865 -865 177 6 -865 -865 -865 165 -15 -865 -865 6 143 -865 177 -865 -15 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TKCKBGSBCVHCTHTTSHMCGCCSGHTGGHMADCCCGTC MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 39 nsites= 4 E= 2.5e+001 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.500000 0.500000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.500000 0.500000 0.000000 0.500000 0.250000 0.250000 0.000000 0.000000 0.750000 0.250000 0.000000 0.500000 0.500000 0.000000 0.000000 0.250000 0.250000 0.500000 0.000000 1.000000 0.000000 0.000000 0.500000 0.250000 0.250000 0.000000 0.250000 0.500000 0.000000 0.250000 0.250000 0.750000 0.000000 0.000000 0.250000 0.000000 0.000000 0.750000 0.250000 0.250000 0.000000 0.500000 0.000000 0.250000 0.000000 0.750000 0.000000 0.000000 0.000000 1.000000 0.000000 0.500000 0.500000 0.000000 0.250000 0.500000 0.000000 0.250000 0.500000 0.500000 0.000000 0.000000 0.000000 0.750000 0.250000 0.000000 0.000000 0.250000 0.750000 0.000000 0.000000 0.750000 0.000000 0.250000 0.000000 1.000000 0.000000 0.000000 0.000000 0.500000 0.500000 0.000000 0.000000 0.000000 1.000000 0.000000 0.250000 0.250000 0.000000 0.500000 0.000000 0.000000 0.250000 0.750000 0.250000 0.000000 0.750000 0.000000 0.000000 0.000000 1.000000 0.000000 0.250000 0.500000 0.000000 0.250000 0.500000 0.500000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.250000 0.000000 0.500000 0.250000 0.250000 0.750000 0.000000 0.000000 0.000000 0.750000 0.250000 0.000000 0.000000 0.750000 0.250000 0.000000 0.000000 0.000000 0.750000 0.250000 0.000000 0.000000 0.250000 0.750000 0.000000 0.750000 0.000000 0.250000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TKCKBGSBCVHCTHTTSHMCGCCSGHTGGHMADCCCGTC MEME-2 regular expression -------------------------------------------------------------------------------- T[GT]C[GT][CGT][GT][CG][TCG]C[ACG][CAT][CA][TA][TAC][TC]T[CG][CAT][AC][CG][GC][CT]C[CG]G[TAC][TG][GA]G[CAT][AC]A[GAT][CA][CG][CG][GT][TG][CT] -------------------------------------------------------------------------------- Time 5.35 secs. ******************************************************************************** ******************************************************************************** MOTIF SCGCGCWGNKMYTMAAMWNCKCSGNRGARA MEME-3 width = 30 sites = 6 llr = 126 E-value = 8.4e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif SCGCGCWGNKMYTMAAMWNCKCSGNRGARA MEME-3 Description -------------------------------------------------------------------------------- Simplified A ::::::7:2:5::5583332:222332a3a pos.-specific C 3828:a::3235:52:5:28:75:3:::2: probability G 72728::a3322::22:22:7237258:5: matrix T ::2:2:3:25:3a:2:253:3::222:::: bits 2.2 * 2.0 * * * * 1.7 * * * * * 1.5 * * * * * * * * Relative 1.3 * *** * * * * ** * Entropy 1.1 ** *** * ** * ** ** * (30.2 bits) 0.9 ******** ** * *** ** * 0.7 ******** **** ** ***** **** 0.4 ******** ***** *** ***** ***** 0.2 ****************** ***** ***** 0.0 ------------------------------ Multilevel GCGCGCAGCTACTAAACTACGCCGAGGAGA consensus C T GGCT C AAT T G CA A sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif SCGCGCWGNKMYTMAAMWNCKCSGNRGARA MEME-3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------------------------ seq26_BACSU 10 1.05e-11 GGCGGGGAT CCGCGCAGGGCCTCAACGTCTCAGCTGAAA ATAACCACGG seq38_BACSU 47 1.46e-11 TGTCAAGCGC GCCCGCAGACAGTACACTACGCGGCAGAGA ATGCCCCATG seq17_BACSU 18 1.17e-10 CTGGAATCAG CCTCGCAGCTATTAAAATGCTACGTGGAAA TGGTACACTC seq4_BACSU 55 1.92e-10 GTAAAATGGG GGGCGCTGCGCCTCGATAACGCCTGAGAGA GAGAAAGAAA seq5_BACSU 45 4.67e-10 AGTGATAGCC GCGCTCTGTTGTTAAAATTAGCGGAGGACA AGAATACAGG seq12_BACSU 49 9.02e-10 TCAGTCAGCA GCGGGCAGGTACTCTGCACCGGCAAGAAGA GGATTTGTCA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif SCGCGCWGNKMYTMAAMWNCKCSGNRGARA MEME-3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- seq26_BACSU 1.1e-11 9_[+3]_61 seq38_BACSU 1.5e-11 46_[+3]_24 seq17_BACSU 1.2e-10 17_[+3]_53 seq4_BACSU 1.9e-10 54_[+3]_16 seq5_BACSU 4.7e-10 44_[+3]_26 seq12_BACSU 9e-10 48_[+3]_22 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif SCGCGCWGNKMYTMAAMWNCKCSGNRGARA MEME-3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF SCGCGCWGNKMYTMAAMWNCKCSGNRGARA width=30 seqs=6 seq26_BACSU ( 10) CCGCGCAGGGCCTCAACGTCTCAGCTGAAA 1 seq38_BACSU ( 47) GCCCGCAGACAGTACACTACGCGGCAGAGA 1 seq17_BACSU ( 18) CCTCGCAGCTATTAAAATGCTACGTGGAAA 1 seq4_BACSU ( 55) GGGCGCTGCGCCTCGATAACGCCTGAGAGA 1 seq5_BACSU ( 45) GCGCTCTGTTGTTAAAATTAGCGGAGGACA 1 seq12_BACSU ( 49) GCGGGCAGGTACTCTGCACCGGCAAGAAGA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif SCGCGCWGNKMYTMAAMWNCKCSGNRGARA MEME-3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 30 n= 3550 bayes= 9.65431 E= 8.4e+001 -923 60 148 -923 -923 192 -52 -923 -923 -40 148 -73 -923 192 -52 -923 -923 -923 180 -73 -923 219 -923 -923 134 -923 -923 26 -923 -923 206 -923 -66 60 48 -73 -923 -40 48 85 92 60 -52 -923 -923 119 -52 26 -923 -923 -923 185 92 119 -923 -923 92 -40 -52 -73 166 -923 -52 -923 34 119 -923 -73 34 -923 -52 85 34 -40 -52 26 -66 192 -923 -923 -923 -923 148 26 -66 160 -52 -923 -66 119 48 -923 -66 -923 148 -73 34 60 -52 -73 34 -923 106 -73 -66 -923 180 -923 192 -923 -923 -923 34 -40 106 -923 192 -923 -923 -923 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif SCGCGCWGNKMYTMAAMWNCKCSGNRGARA MEME-3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 30 nsites= 6 E= 8.4e+001 0.000000 0.333333 0.666667 0.000000 0.000000 0.833333 0.166667 0.000000 0.000000 0.166667 0.666667 0.166667 0.000000 0.833333 0.166667 0.000000 0.000000 0.000000 0.833333 0.166667 0.000000 1.000000 0.000000 0.000000 0.666667 0.000000 0.000000 0.333333 0.000000 0.000000 1.000000 0.000000 0.166667 0.333333 0.333333 0.166667 0.000000 0.166667 0.333333 0.500000 0.500000 0.333333 0.166667 0.000000 0.000000 0.500000 0.166667 0.333333 0.000000 0.000000 0.000000 1.000000 0.500000 0.500000 0.000000 0.000000 0.500000 0.166667 0.166667 0.166667 0.833333 0.000000 0.166667 0.000000 0.333333 0.500000 0.000000 0.166667 0.333333 0.000000 0.166667 0.500000 0.333333 0.166667 0.166667 0.333333 0.166667 0.833333 0.000000 0.000000 0.000000 0.000000 0.666667 0.333333 0.166667 0.666667 0.166667 0.000000 0.166667 0.500000 0.333333 0.000000 0.166667 0.000000 0.666667 0.166667 0.333333 0.333333 0.166667 0.166667 0.333333 0.000000 0.500000 0.166667 0.166667 0.000000 0.833333 0.000000 1.000000 0.000000 0.000000 0.000000 0.333333 0.166667 0.500000 0.000000 1.000000 0.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif SCGCGCWGNKMYTMAAMWNCKCSGNRGARA MEME-3 regular expression -------------------------------------------------------------------------------- [GC]CGCGC[AT]G[CG][TG][AC][CT]T[AC]AA[CA][TA][AT]C[GT]C[CG]G[AC][GA]GA[GA]A -------------------------------------------------------------------------------- Time 7.80 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- seq1_BACSU 7.59e-01 100 seq2_BACSU 3.00e-01 100 seq3_BACSU 1.74e-01 100 seq4_BACSU 1.74e-06 54_[+3(1.92e-10)]_16 seq5_BACSU 3.32e-06 44_[+3(4.67e-10)]_26 seq6_BACSU 2.17e-01 100 seq7_BACSU 9.88e-07 50_[+1(7.97e-10)]_22 seq8_BACSU 2.86e-14 21_[+2(5.97e-18)]_40 seq9_BACSU 3.07e-01 100 seq10_BACSU 9.51e-06 45_[+1(3.02e-09)]_27 seq11_BACSU 5.42e-01 100 seq12_BACSU 1.14e-06 48_[+3(9.02e-10)]_22 seq13_BACSU 3.60e-06 51_[+1(1.94e-08)]_21 seq14_BACSU 9.10e-01 100 seq15_BACSU 9.21e-01 100 seq16_BACSU 5.27e-01 100 seq17_BACSU 4.30e-07 17_[+3(1.17e-10)]_53 seq18_BACSU 6.77e-01 100 seq19_BACSU 4.91e-01 100 seq20_BACSU 3.42e-01 100 seq21_BACSU 8.53e-01 100 seq22_BACSU 1.15e-01 100 seq23_BACSU 1.86e-03 58_[+1(3.85e-05)]_14 seq24_BACSU 7.66e-01 100 seq25_BACSU 3.30e-01 100 seq26_BACSU 4.21e-08 9_[+3(1.05e-11)]_61 seq27_BACSU 1.00e-05 58_[+1(2.24e-09)]_14 seq28_BACSU 7.58e-11 10_[+2(1.16e-14)]_51 seq29_BACSU 2.10e-11 6_[+2(1.20e-15)]_55 seq30_BACSU 1.33e-01 100 seq31_BACSU 3.49e-01 100 seq32_BACSU 2.77e-01 100 seq33_BACSU 1.09e-05 54_[+1(4.34e-09)]_18 seq34_BACSU 5.04e-01 100 seq35_BACSU 4.51e-01 100 seq36_BACSU 1.08e-10 42_[+2(5.63e-15)]_19 seq37_BACSU 3.31e-01 100 seq38_BACSU 5.48e-09 46_[+3(1.46e-11)]_24 seq39_BACSU 3.29e-07 47_[+1(1.07e-10)]_25 seq40_BACSU 5.59e-02 46_[+1(6.69e-05)]_26 seq41_BACSU 8.32e-02 100 seq42_BACSU 1.66e-06 47_[+1(2.54e-10)]_25 seq43_BACSU 4.94e-01 100 seq44_BACSU 1.00e+00 100 seq45_BACSU 9.25e-10 11_[+1(1.11e-05)]_13_[+1(2.80e-13)]_\ 20 seq46_BACSU 8.55e-01 100 seq47_BACSU 3.33e-08 50_[+1(1.30e-10)]_22 seq48_BACSU 7.73e-01 100 seq49_BACSU 3.45e-01 100 seq50_BACSU 3.04e-01 100 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (3) found. ******************************************************************************** CPU: kodomo ********************************************************************************