******************************************************************************** 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= housekeeping.fasta CONTROL SEQUENCES= --none-- ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ JKJHJKOE_00002 1.0000 100 JKJHJKOE_00014 1.0000 100 JKJHJKOE_00057 1.0000 100 JKJHJKOE_00058 1.0000 100 JKJHJKOE_00060 1.0000 100 JKJHJKOE_00079 1.0000 100 JKJHJKOE_00089 1.0000 100 JKJHJKOE_00090 1.0000 100 JKJHJKOE_00094 1.0000 100 JKJHJKOE_00102 1.0000 100 JKJHJKOE_00111 1.0000 100 JKJHJKOE_00124 1.0000 100 JKJHJKOE_00167 1.0000 100 JKJHJKOE_00178 1.0000 100 JKJHJKOE_00183 1.0000 100 JKJHJKOE_00184 1.0000 100 JKJHJKOE_00185 1.0000 100 JKJHJKOE_00186 1.0000 100 JKJHJKOE_00187 1.0000 100 JKJHJKOE_00188 1.0000 100 JKJHJKOE_00189 1.0000 100 JKJHJKOE_00190 1.0000 100 JKJHJKOE_00191 1.0000 100 JKJHJKOE_00192 1.0000 100 JKJHJKOE_00193 1.0000 100 JKJHJKOE_00194 1.0000 100 JKJHJKOE_00195 1.0000 100 JKJHJKOE_00196 1.0000 100 JKJHJKOE_00197 1.0000 100 JKJHJKOE_00198 1.0000 100 JKJHJKOE_00199 1.0000 100 JKJHJKOE_00200 1.0000 100 JKJHJKOE_00201 1.0000 100 JKJHJKOE_00202 1.0000 100 JKJHJKOE_00204 1.0000 100 JKJHJKOE_00205 1.0000 100 JKJHJKOE_00206 1.0000 100 JKJHJKOE_00207 1.0000 100 JKJHJKOE_00208 1.0000 100 JKJHJKOE_00230 1.0000 100 JKJHJKOE_00233 1.0000 100 JKJHJKOE_00234 1.0000 100 JKJHJKOE_00235 1.0000 100 JKJHJKOE_00236 1.0000 100 JKJHJKOE_00237 1.0000 100 JKJHJKOE_00238 1.0000 100 JKJHJKOE_00239 1.0000 100 JKJHJKOE_00240 1.0000 100 JKJHJKOE_00241 1.0000 100 JKJHJKOE_00247 1.0000 100 JKJHJKOE_00251 1.0000 100 JKJHJKOE_00252 1.0000 100 JKJHJKOE_00269 1.0000 100 JKJHJKOE_00270 1.0000 100 JKJHJKOE_00277 1.0000 100 JKJHJKOE_00298 1.0000 100 JKJHJKOE_00332 1.0000 100 JKJHJKOE_00415 1.0000 100 JKJHJKOE_00416 1.0000 100 JKJHJKOE_00434 1.0000 100 JKJHJKOE_00442 1.0000 100 JKJHJKOE_00445 1.0000 100 JKJHJKOE_00475 1.0000 100 JKJHJKOE_00494 1.0000 100 JKJHJKOE_00505 1.0000 100 JKJHJKOE_00509 1.0000 100 JKJHJKOE_00516 1.0000 100 JKJHJKOE_00571 1.0000 100 JKJHJKOE_00582 1.0000 100 JKJHJKOE_00590 1.0000 100 JKJHJKOE_00591 1.0000 100 JKJHJKOE_00630 1.0000 100 JKJHJKOE_00655 1.0000 100 JKJHJKOE_00689 1.0000 100 JKJHJKOE_00697 1.0000 100 JKJHJKOE_00698 1.0000 100 JKJHJKOE_00731 1.0000 100 JKJHJKOE_00732 1.0000 100 JKJHJKOE_00733 1.0000 100 JKJHJKOE_00745 1.0000 100 JKJHJKOE_00753 1.0000 100 JKJHJKOE_00790 1.0000 100 JKJHJKOE_00828 1.0000 100 JKJHJKOE_00829 1.0000 100 JKJHJKOE_00830 1.0000 100 JKJHJKOE_00853 1.0000 100 JKJHJKOE_00862 1.0000 100 JKJHJKOE_00866 1.0000 100 JKJHJKOE_00867 1.0000 100 JKJHJKOE_00877 1.0000 100 JKJHJKOE_00881 1.0000 100 JKJHJKOE_00897 1.0000 100 JKJHJKOE_00924 1.0000 100 JKJHJKOE_00980 1.0000 100 JKJHJKOE_00987 1.0000 100 JKJHJKOE_00990 1.0000 100 JKJHJKOE_00999 1.0000 100 JKJHJKOE_01000 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 housekeeping.fasta -dna -nmotifs 3 -minw 6 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= 98 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= 9800 N= 98 sample: seed= 0 hsfrac= 0 searchsize= 9800 norand= no csites= 1000 Letter frequencies in dataset: A 0.232 C 0.232 G 0.294 T 0.241 Background letter frequencies (from file dataset with add-one prior applied): A 0.232 C 0.232 G 0.294 T 0.241 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF MTTYYCYYTCYTCCT MEME-1 width = 15 sites = 20 llr = 211 E-value = 5.1e-004 ******************************************************************************** -------------------------------------------------------------------------------- Motif MTTYYCYYTCYTCCT MEME-1 Description -------------------------------------------------------------------------------- Simplified A 5:::1:1::11:::1 pos.-specific C 42:559451943981 probability G :2:1::223:1:1:: matrix T 27a451447158129 bits 2.1 * 1.9 * 1.7 * * 1.5 * * * Relative 1.3 * * * **** Entropy 1.1 * * * **** (15.2 bits) 0.8 * ** ** **** 0.6 ****** *** **** 0.4 ****** ******** 0.2 *************** 0.0 --------------- Multilevel ATTCTCTCTCTTCCT consensus CG TC CTG CC T sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif MTTYYCYYTCYTCCT MEME-1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------- JKJHJKOE_00732 4 5.10e-08 CAT ATTCTCGTTCTTCCT AATGGTGGCT JKJHJKOE_00591 53 1.53e-07 CACGCACACC ACTTTCTCTCTTCCT ACTCTCGGAG JKJHJKOE_00247 45 4.69e-07 GGGCGTGTCT TTTCCCTCTCTTCTT TTCTTGGGTT JKJHJKOE_00828 79 8.32e-07 CACCGTTCGC ACTCTCCTGCCTCCT CGCACCA JKJHJKOE_00494 47 8.32e-07 TTCCCTCGTT TTTCCCCTTCCTCTT CCCACTGACT JKJHJKOE_00924 82 1.04e-06 GCACAAGAAT CGTCCCCCTCCTCTT TAGC JKJHJKOE_00571 86 1.92e-06 GACTCTATCC CTTCCCCGTCTTCCC JKJHJKOE_00866 76 2.94e-06 CAAACTTATG CTTCTCTTGCTCCTT ATCCTCTCGA JKJHJKOE_00434 62 4.19e-06 CGTTTTAGGT ATTCTCTTTCCCGCT GCTATGATGG JKJHJKOE_00111 53 5.51e-06 CGTTTCGCTC CTTTTCTGTATTCCT TTCGTGGGAT JKJHJKOE_00277 35 8.69e-06 GAGAGAGAGA AGTTTCGTTCATCCT CGCACCCGTT JKJHJKOE_00980 83 9.42e-06 ACCACGGCAG ACTGTCCCCCTTCCT AGT JKJHJKOE_00829 84 1.02e-05 ACAACAACCT ATTTCCCCTCTTTCA TA JKJHJKOE_00745 1 1.02e-05 . CGTCCCCTCCGTCCT CACGAAAGCC JKJHJKOE_00178 60 1.10e-05 TGTGCGTCGG CTTCTTTGTCGTCCT GTTACAGCTG JKJHJKOE_00733 35 1.18e-05 ACGCAAGGTG ATTGCCACGCTCCCT ACCGACGCAG JKJHJKOE_01000 86 1.49e-05 TCGCACACCT ATTTCCTCGTCTCCC JKJHJKOE_00862 86 1.75e-05 CAAGCTCATC CTTTCCTCTTCCTCT JKJHJKOE_00183 23 2.19e-05 TTCATTTCGC TTTTTTGTGCCTCCT TGTTGCGTGC JKJHJKOE_00897 85 2.88e-05 GAGCCAAACG CGTTACACTCCCCCT C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif MTTYYCYYTCYTCCT MEME-1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- JKJHJKOE_00732 5.1e-08 3_[+1]_82 JKJHJKOE_00591 1.5e-07 52_[+1]_33 JKJHJKOE_00247 4.7e-07 44_[+1]_41 JKJHJKOE_00828 8.3e-07 78_[+1]_7 JKJHJKOE_00494 8.3e-07 46_[+1]_39 JKJHJKOE_00924 1e-06 81_[+1]_4 JKJHJKOE_00571 1.9e-06 85_[+1] JKJHJKOE_00866 2.9e-06 75_[+1]_10 JKJHJKOE_00434 4.2e-06 61_[+1]_24 JKJHJKOE_00111 5.5e-06 52_[+1]_33 JKJHJKOE_00277 8.7e-06 34_[+1]_51 JKJHJKOE_00980 9.4e-06 82_[+1]_3 JKJHJKOE_00829 1e-05 83_[+1]_2 JKJHJKOE_00745 1e-05 [+1]_85 JKJHJKOE_00178 1.1e-05 59_[+1]_26 JKJHJKOE_00733 1.2e-05 34_[+1]_51 JKJHJKOE_01000 1.5e-05 85_[+1] JKJHJKOE_00862 1.7e-05 85_[+1] JKJHJKOE_00183 2.2e-05 22_[+1]_63 JKJHJKOE_00897 2.9e-05 84_[+1]_1 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif MTTYYCYYTCYTCCT MEME-1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF MTTYYCYYTCYTCCT width=15 seqs=20 JKJHJKOE_00732 ( 4) ATTCTCGTTCTTCCT 1 JKJHJKOE_00591 ( 53) ACTTTCTCTCTTCCT 1 JKJHJKOE_00247 ( 45) TTTCCCTCTCTTCTT 1 JKJHJKOE_00828 ( 79) ACTCTCCTGCCTCCT 1 JKJHJKOE_00494 ( 47) TTTCCCCTTCCTCTT 1 JKJHJKOE_00924 ( 82) CGTCCCCCTCCTCTT 1 JKJHJKOE_00571 ( 86) CTTCCCCGTCTTCCC 1 JKJHJKOE_00866 ( 76) CTTCTCTTGCTCCTT 1 JKJHJKOE_00434 ( 62) ATTCTCTTTCCCGCT 1 JKJHJKOE_00111 ( 53) CTTTTCTGTATTCCT 1 JKJHJKOE_00277 ( 35) AGTTTCGTTCATCCT 1 JKJHJKOE_00980 ( 83) ACTGTCCCCCTTCCT 1 JKJHJKOE_00829 ( 84) ATTTCCCCTCTTTCA 1 JKJHJKOE_00745 ( 1) CGTCCCCTCCGTCCT 1 JKJHJKOE_00178 ( 60) CTTCTTTGTCGTCCT 1 JKJHJKOE_00733 ( 35) ATTGCCACGCTCCCT 1 JKJHJKOE_01000 ( 86) ATTTCCTCGTCTCCC 1 JKJHJKOE_00862 ( 86) CTTTCCTCTTCCTCT 1 JKJHJKOE_00183 ( 23) TTTTTTGTGCCTCCT 1 JKJHJKOE_00897 ( 85) CGTTACACTCCCCCT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif MTTYYCYYTCYTCCT MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 8428 bayes= 8.96771 E= 5.1e-004 95 78 -1097 -68 -1097 -63 -56 143 -1097 -1097 -1097 205 -1097 111 -156 73 -221 95 -1097 105 -1097 195 -1097 -127 -122 59 -97 73 -1097 95 -97 73 -1097 -122 -23 143 -221 187 -1097 -127 -221 78 -156 90 -1097 11 -1097 164 -1097 187 -255 -127 -1097 178 -1097 -27 -221 -122 -1097 182 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif MTTYYCYYTCYTCCT MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 20 E= 5.1e-004 0.450000 0.400000 0.000000 0.150000 0.000000 0.150000 0.200000 0.650000 0.000000 0.000000 0.000000 1.000000 0.000000 0.500000 0.100000 0.400000 0.050000 0.450000 0.000000 0.500000 0.000000 0.900000 0.000000 0.100000 0.100000 0.350000 0.150000 0.400000 0.000000 0.450000 0.150000 0.400000 0.000000 0.100000 0.250000 0.650000 0.050000 0.850000 0.000000 0.100000 0.050000 0.400000 0.100000 0.450000 0.000000 0.250000 0.000000 0.750000 0.000000 0.850000 0.050000 0.100000 0.000000 0.800000 0.000000 0.200000 0.050000 0.100000 0.000000 0.850000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif MTTYYCYYTCYTCCT MEME-1 regular expression -------------------------------------------------------------------------------- [AC][TG]T[CT][TC]C[TC][CT][TG]C[TC][TC]C[CT]T -------------------------------------------------------------------------------- Time 6.86 secs. ******************************************************************************** ******************************************************************************** MOTIF SGTKKTTWRKASTTWTWTGSGWMAKAARGAGRARAYW MEME-2 width = 37 sites = 6 llr = 166 E-value = 1.4e+000 ******************************************************************************** -------------------------------------------------------------------------------- Motif SGTKKTTWRKASTTWTWTGSGWMAKAARGAGRARAYW MEME-2 Description -------------------------------------------------------------------------------- Simplified A :2:::2:73:7:2:3:3222:53a:883:825758:7 pos.-specific C 3:::2::::::3:2::::252:5:2::::2::::25: probability G 78:53:2:7325:::2::7372::3:27a:8325:2: matrix T ::a55883:722887878::232:52:::::22::33 bits 2.1 * * 1.9 * * 1.7 * * * 1.5 * * ** * * ** ** * Relative 1.3 ** *** ** * * * ** *** * * Entropy 1.1 *** ***** ****** * ****** * * (39.9 bits) 0.8 **** ****** ****** * ****** *** * 0.6 **** ****** ************ ****** ***** 0.4 ************************************* 0.2 ************************************* 0.0 ------------------------------------- Multilevel GGTGTTTAGTAGTTTTTTGCGACATAAGGAGAAAACA consensus C TG TAG C A A G TA G A G G TT sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif SGTKKTTWRKASTTWTWTGSGWMAKAARGAGRARAYW MEME-2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------------------------------- JKJHJKOE_00194 35 3.81e-16 GTCAAATTGC GGTGGTTAATACTTTTTTGCGACATAAAGAGTTGACT GAACTAGAAA JKJHJKOE_00234 62 8.34e-15 GTTGGTTTCG GGTGTTTTGTTGTTTTTTACGTCATAAGGAGAGGCCA GT JKJHJKOE_00208 63 7.56e-14 ACCATGTGGG GGTTGTTAGTAGACTGATGCGACAGAAGGAAGAAATA G JKJHJKOE_00237 62 4.33e-13 TCTTCCTGTC CGTTTATAGGGGTTATTTCGCATACAAGGAGAAGATA AT JKJHJKOE_00002 60 7.08e-13 GATACGACTA CATTCTTTATACTTATAAGATTAATAAGGAGGAAACT AACT JKJHJKOE_00240 64 3.88e-12 CAAGGTTTAC GGTGTTGAGGATTTTTTTGGGGAAGTGAGCGAAAAGA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif SGTKKTTWRKASTTWTWTGSGWMAKAARGAGRARAYW MEME-2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- JKJHJKOE_00194 3.8e-16 34_[+2]_29 JKJHJKOE_00234 8.3e-15 61_[+2]_2 JKJHJKOE_00208 7.6e-14 62_[+2]_1 JKJHJKOE_00237 4.3e-13 61_[+2]_2 JKJHJKOE_00002 7.1e-13 59_[+2]_4 JKJHJKOE_00240 3.9e-12 63_[+2] -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif SGTKKTTWRKASTTWTWTGSGWMAKAARGAGRARAYW MEME-2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF SGTKKTTWRKASTTWTWTGSGWMAKAARGAGRARAYW width=37 seqs=6 JKJHJKOE_00194 ( 35) GGTGGTTAATACTTTTTTGCGACATAAAGAGTTGACT 1 JKJHJKOE_00234 ( 62) GGTGTTTTGTTGTTTTTTACGTCATAAGGAGAGGCCA 1 JKJHJKOE_00208 ( 63) GGTTGTTAGTAGACTGATGCGACAGAAGGAAGAAATA 1 JKJHJKOE_00237 ( 62) CGTTTATAGGGGTTATTTCGCATACAAGGAGAAGATA 1 JKJHJKOE_00002 ( 60) CATTCTTTATACTTATAAGATTAATAAGGAGGAAACT 1 JKJHJKOE_00240 ( 64) GGTGTTGAGGATTTTTTTGGGGAAGTGAGCGAAAAGA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif SGTKKTTWRKASTTWTWTGSGWMAKAARGAGRARAYW MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 37 n= 6272 bayes= 10.4762 E= 1.4e+000 -923 52 118 -923 -48 -923 150 -923 -923 -923 -923 205 -923 -923 76 105 -923 -48 18 105 -48 -923 -923 179 -923 -923 -82 179 152 -923 -923 47 52 -923 118 -923 -923 -923 18 147 152 -923 -82 -53 -923 52 76 -53 -48 -923 -923 179 -923 -48 -923 179 52 -923 -923 147 -923 -923 -82 179 52 -923 -923 147 -48 -923 -923 179 -48 -48 118 -923 -48 110 18 -923 -923 -48 118 -53 110 -923 -82 47 52 110 -923 -53 210 -923 -923 -923 -923 -48 18 105 184 -923 -923 -53 184 -923 -82 -923 52 -923 118 -923 -923 -923 176 -923 184 -48 -923 -923 -48 -923 150 -923 110 -923 18 -53 152 -923 -82 -53 110 -923 76 -923 184 -48 -923 -923 -923 110 -82 47 152 -923 -923 47 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif SGTKKTTWRKASTTWTWTGSGWMAKAARGAGRARAYW MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 37 nsites= 6 E= 1.4e+000 0.000000 0.333333 0.666667 0.000000 0.166667 0.000000 0.833333 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.500000 0.500000 0.000000 0.166667 0.333333 0.500000 0.166667 0.000000 0.000000 0.833333 0.000000 0.000000 0.166667 0.833333 0.666667 0.000000 0.000000 0.333333 0.333333 0.000000 0.666667 0.000000 0.000000 0.000000 0.333333 0.666667 0.666667 0.000000 0.166667 0.166667 0.000000 0.333333 0.500000 0.166667 0.166667 0.000000 0.000000 0.833333 0.000000 0.166667 0.000000 0.833333 0.333333 0.000000 0.000000 0.666667 0.000000 0.000000 0.166667 0.833333 0.333333 0.000000 0.000000 0.666667 0.166667 0.000000 0.000000 0.833333 0.166667 0.166667 0.666667 0.000000 0.166667 0.500000 0.333333 0.000000 0.000000 0.166667 0.666667 0.166667 0.500000 0.000000 0.166667 0.333333 0.333333 0.500000 0.000000 0.166667 1.000000 0.000000 0.000000 0.000000 0.000000 0.166667 0.333333 0.500000 0.833333 0.000000 0.000000 0.166667 0.833333 0.000000 0.166667 0.000000 0.333333 0.000000 0.666667 0.000000 0.000000 0.000000 1.000000 0.000000 0.833333 0.166667 0.000000 0.000000 0.166667 0.000000 0.833333 0.000000 0.500000 0.000000 0.333333 0.166667 0.666667 0.000000 0.166667 0.166667 0.500000 0.000000 0.500000 0.000000 0.833333 0.166667 0.000000 0.000000 0.000000 0.500000 0.166667 0.333333 0.666667 0.000000 0.000000 0.333333 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif SGTKKTTWRKASTTWTWTGSGWMAKAARGAGRARAYW MEME-2 regular expression -------------------------------------------------------------------------------- [GC]GT[GT][TG]TT[AT][GA][TG]A[GC]TT[TA]T[TA]TG[CG]G[AT][CA]A[TG]AA[GA]GAG[AG]A[AG]A[CT][AT] -------------------------------------------------------------------------------- Time 13.33 secs. ******************************************************************************** ******************************************************************************** MOTIF AAAGTRAGGGG MEME-3 width = 11 sites = 10 llr = 112 E-value = 2.0e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif AAAGTRAGGGG MEME-3 Description -------------------------------------------------------------------------------- Simplified A a99:339::1: pos.-specific C :::::21:::: probability G :11a:5:aa97 matrix T ::::7:::::3 bits 2.1 * 1.9 * 1.7 **** *** 1.5 **** *** Relative 1.3 ***** **** Entropy 1.1 ***** ***** (16.2 bits) 0.8 ***** ***** 0.6 ***** ***** 0.4 *********** 0.2 *********** 0.0 ----------- Multilevel AAAGTGAGGGG consensus AA T sequence C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAAGTRAGGGG MEME-3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ----------- JKJHJKOE_00206 76 8.07e-07 CTGGAAAGAA AAAGTAAGGGG ATCAGGAGGG JKJHJKOE_00189 85 8.07e-07 TGTCAAAGAG AAAGTAAGGGG GGGGT JKJHJKOE_00200 74 1.53e-06 GTAAGGTAGG AAAGTCAGGGG TAAAGTAGAG JKJHJKOE_00197 66 1.53e-06 AAACGGTAAG AAAGTGAGGGT ATGTCGTAAA JKJHJKOE_00014 84 1.53e-06 GGATAGCGTG AAAGTGAGGGT GAAGTA JKJHJKOE_00194 80 1.97e-06 CTGAACTAGA AAAGAGAGGGG TTCGGGAGTG JKJHJKOE_00241 49 6.74e-06 GCGGTCGTTC AAAGTACGGGG CTAAGCGCCC JKJHJKOE_00090 46 1.23e-05 GGGGAATGTA AAGGTGAGGGT GTTCAGAGCG JKJHJKOE_00505 39 1.38e-05 AATTGTGACA AGAGAGAGGGG AACAGAATCT JKJHJKOE_00591 11 1.62e-05 CCCTGCGCAA AAAGACAGGAG AGCTCTTATA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAAGTRAGGGG MEME-3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- JKJHJKOE_00206 8.1e-07 75_[+3]_14 JKJHJKOE_00189 8.1e-07 84_[+3]_5 JKJHJKOE_00200 1.5e-06 73_[+3]_16 JKJHJKOE_00197 1.5e-06 65_[+3]_24 JKJHJKOE_00014 1.5e-06 83_[+3]_6 JKJHJKOE_00194 2e-06 79_[+3]_10 JKJHJKOE_00241 6.7e-06 48_[+3]_41 JKJHJKOE_00090 1.2e-05 45_[+3]_44 JKJHJKOE_00505 1.4e-05 38_[+3]_51 JKJHJKOE_00591 1.6e-05 10_[+3]_79 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAAGTRAGGGG MEME-3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF AAAGTRAGGGG width=11 seqs=10 JKJHJKOE_00206 ( 76) AAAGTAAGGGG 1 JKJHJKOE_00189 ( 85) AAAGTAAGGGG 1 JKJHJKOE_00200 ( 74) AAAGTCAGGGG 1 JKJHJKOE_00197 ( 66) AAAGTGAGGGT 1 JKJHJKOE_00014 ( 84) AAAGTGAGGGT 1 JKJHJKOE_00194 ( 80) AAAGAGAGGGG 1 JKJHJKOE_00241 ( 49) AAAGTACGGGG 1 JKJHJKOE_00090 ( 46) AAGGTGAGGGT 1 JKJHJKOE_00505 ( 39) AGAGAGAGGGG 1 JKJHJKOE_00591 ( 11) AAAGACAGGAG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAAGTRAGGGG MEME-3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 11 n= 8820 bayes= 10.7272 E= 2.0e+001 210 -997 -997 -997 195 -997 -155 -997 195 -997 -155 -997 -997 -997 176 -997 37 -997 -997 154 37 -22 76 -997 195 -121 -997 -997 -997 -997 176 -997 -997 -997 176 -997 -122 -997 161 -997 -997 -997 125 32 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAAGTRAGGGG MEME-3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 11 nsites= 10 E= 2.0e+001 1.000000 0.000000 0.000000 0.000000 0.900000 0.000000 0.100000 0.000000 0.900000 0.000000 0.100000 0.000000 0.000000 0.000000 1.000000 0.000000 0.300000 0.000000 0.000000 0.700000 0.300000 0.200000 0.500000 0.000000 0.900000 0.100000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.100000 0.000000 0.900000 0.000000 0.000000 0.000000 0.700000 0.300000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAAGTRAGGGG MEME-3 regular expression -------------------------------------------------------------------------------- AAAG[TA][GAC]AGGG[GT] -------------------------------------------------------------------------------- Time 19.66 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- JKJHJKOE_00002 6.54e-09 59_[+2(7.08e-13)]_4 JKJHJKOE_00014 3.02e-04 83_[+3(1.53e-06)]_6 JKJHJKOE_00057 4.21e-01 100 JKJHJKOE_00058 2.56e-02 100 JKJHJKOE_00060 9.93e-01 100 JKJHJKOE_00079 1.35e-01 100 JKJHJKOE_00089 6.88e-01 100 JKJHJKOE_00090 2.55e-02 45_[+3(1.23e-05)]_44 JKJHJKOE_00094 6.65e-01 100 JKJHJKOE_00102 2.25e-01 100 JKJHJKOE_00111 1.01e-02 52_[+1(5.51e-06)]_33 JKJHJKOE_00124 3.96e-01 100 JKJHJKOE_00167 1.74e-01 100 JKJHJKOE_00178 2.83e-02 59_[+1(1.10e-05)]_26 JKJHJKOE_00183 2.17e-02 22_[+1(2.19e-05)]_63 JKJHJKOE_00184 1.29e-01 100 JKJHJKOE_00185 5.11e-01 100 JKJHJKOE_00186 1.58e-01 100 JKJHJKOE_00187 5.40e-01 100 JKJHJKOE_00188 7.57e-02 100 JKJHJKOE_00189 3.01e-04 84_[+3(8.07e-07)]_5 JKJHJKOE_00190 1.82e-01 100 JKJHJKOE_00191 1.08e-01 100 JKJHJKOE_00192 2.50e-01 100 JKJHJKOE_00193 6.87e-01 100 JKJHJKOE_00194 4.28e-16 34_[+2(3.81e-16)]_8_[+3(1.97e-06)]_\ 10 JKJHJKOE_00195 1.06e-01 100 JKJHJKOE_00196 5.46e-02 100 JKJHJKOE_00197 2.40e-04 65_[+3(1.53e-06)]_24 JKJHJKOE_00198 9.46e-02 100 JKJHJKOE_00199 9.84e-02 100 JKJHJKOE_00200 2.88e-03 24_[+3(4.09e-05)]_38_[+3(1.53e-06)]_\ 16 JKJHJKOE_00201 7.00e-01 100 JKJHJKOE_00202 9.56e-01 100 JKJHJKOE_00204 1.37e-01 100 JKJHJKOE_00205 1.85e-01 100 JKJHJKOE_00206 5.13e-04 75_[+3(8.07e-07)]_14 JKJHJKOE_00207 6.34e-01 100 JKJHJKOE_00208 1.22e-09 62_[+2(7.56e-14)]_1 JKJHJKOE_00230 6.38e-01 100 JKJHJKOE_00233 8.77e-01 100 JKJHJKOE_00234 6.09e-12 61_[+2(8.34e-15)]_2 JKJHJKOE_00235 7.42e-01 100 JKJHJKOE_00236 4.46e-01 100 JKJHJKOE_00237 7.11e-11 61_[+2(4.33e-13)]_2 JKJHJKOE_00238 2.15e-01 100 JKJHJKOE_00239 6.87e-01 100 JKJHJKOE_00240 1.81e-08 63_[+2(3.88e-12)] JKJHJKOE_00241 1.14e-02 48_[+3(6.74e-06)]_41 JKJHJKOE_00247 1.76e-05 3_[+3(3.99e-05)]_30_[+1(4.69e-07)]_\ 41 JKJHJKOE_00251 8.72e-01 100 JKJHJKOE_00252 4.68e-01 100 JKJHJKOE_00269 6.75e-01 100 JKJHJKOE_00270 1.49e-01 100 JKJHJKOE_00277 2.47e-03 34_[+1(8.69e-06)]_51 JKJHJKOE_00298 9.47e-02 100 JKJHJKOE_00332 3.63e-01 100 JKJHJKOE_00415 9.77e-03 100 JKJHJKOE_00416 5.75e-01 100 JKJHJKOE_00434 3.61e-03 61_[+1(4.19e-06)]_24 JKJHJKOE_00442 4.29e-02 100 JKJHJKOE_00445 1.14e-01 100 JKJHJKOE_00475 1.38e-02 59_[+2(7.94e-05)]_4 JKJHJKOE_00494 1.58e-03 46_[+1(8.32e-07)]_39 JKJHJKOE_00505 2.71e-02 38_[+3(1.38e-05)]_51 JKJHJKOE_00509 2.21e-01 100 JKJHJKOE_00516 5.26e-01 100 JKJHJKOE_00571 6.60e-03 85_[+1(1.92e-06)] JKJHJKOE_00582 3.50e-01 100 JKJHJKOE_00590 9.25e-01 100 JKJHJKOE_00591 3.09e-06 10_[+3(1.62e-05)]_31_[+1(1.53e-07)]_\ 33 JKJHJKOE_00630 4.53e-01 100 JKJHJKOE_00655 3.04e-01 100 JKJHJKOE_00689 9.95e-01 100 JKJHJKOE_00697 1.60e-01 100 JKJHJKOE_00698 8.44e-01 100 JKJHJKOE_00731 3.32e-01 100 JKJHJKOE_00732 3.03e-04 3_[+1(5.10e-08)]_82 JKJHJKOE_00733 2.49e-02 34_[+1(1.18e-05)]_51 JKJHJKOE_00745 1.84e-02 [+1(1.02e-05)]_85 JKJHJKOE_00753 3.77e-01 100 JKJHJKOE_00790 4.12e-01 100 JKJHJKOE_00828 7.97e-04 78_[+1(8.32e-07)]_7 JKJHJKOE_00829 6.57e-03 83_[+1(1.02e-05)]_2 JKJHJKOE_00830 5.21e-01 100 JKJHJKOE_00853 5.02e-01 100 JKJHJKOE_00862 1.45e-02 85_[+1(1.75e-05)] JKJHJKOE_00866 9.54e-04 75_[+1(2.94e-06)]_10 JKJHJKOE_00867 6.52e-01 100 JKJHJKOE_00877 5.17e-01 100 JKJHJKOE_00881 7.54e-01 100 JKJHJKOE_00897 3.68e-02 84_[+1(2.88e-05)]_1 JKJHJKOE_00924 2.02e-03 81_[+1(1.04e-06)]_4 JKJHJKOE_00980 7.10e-03 82_[+1(9.42e-06)]_3 JKJHJKOE_00987 7.90e-01 100 JKJHJKOE_00990 4.77e-01 100 JKJHJKOE_00999 4.03e-01 100 JKJHJKOE_01000 1.19e-02 85_[+1(1.49e-05)] -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (3) found. ******************************************************************************** CPU: kodomo ********************************************************************************