******************************************************************************** MEME - Motif discovery tool ******************************************************************************** MEME version 5.4.1 (Release date: Sat Aug 21 19:23:23 2021 -0700) 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= promotors-test.fasta CONTROL SEQUENCES= --none-- ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 21promotor 1.0000 150 85promotor 1.0000 150 114promotor 1.0000 150 119promotor 1.0000 150 142promotor 1.0000 150 143promotor 1.0000 150 151promotor 1.0000 150 170promotor 1.0000 150 185promotor 1.0000 150 194promotor 1.0000 150 240promotor 1.0000 150 242promotor 1.0000 150 277promotor 1.0000 150 287promotor 1.0000 150 308promotor 1.0000 150 309promotor 1.0000 150 331promotor 1.0000 150 352promotor 1.0000 150 353promotor 1.0000 150 421promotor 1.0000 150 440promotor 1.0000 150 448promotor 1.0000 150 458promotor 1.0000 150 459promotor 1.0000 150 462promotor 1.0000 150 496promotor 1.0000 150 504promotor 1.0000 150 526promotor 1.0000 150 530promotor 1.0000 150 540promotor 1.0000 150 544promotor 1.0000 150 549promotor 1.0000 150 551promotor 1.0000 150 560promotor 1.0000 150 597promotor 1.0000 150 598promotor 1.0000 150 599promotor 1.0000 150 611promotor 1.0000 150 671promotor 1.0000 150 729promotor 1.0000 150 752promotor 1.0000 150 769promotor 1.0000 150 795promotor 1.0000 150 797promotor 1.0000 150 799promotor 1.0000 150 821promotor 1.0000 150 831promotor 1.0000 150 837promotor 1.0000 150 843promotor 1.0000 150 854promotor 1.0000 150 867promotor 1.0000 150 875promotor 1.0000 150 900promotor 1.0000 150 904promotor 1.0000 150 926promotor 1.0000 150 959promotor 1.0000 150 985promotor 1.0000 150 1038promotor 1.0000 150 1048promotor 1.0000 150 1074promotor 1.0000 150 1099promotor 1.0000 150 1103promotor 1.0000 150 1109promotor 1.0000 150 1139promotor 1.0000 150 1205promotor 1.0000 150 1254promotor 1.0000 150 1265promotor 1.0000 150 1273promotor 1.0000 150 1404promotor 1.0000 150 1416promotor 1.0000 150 1508promotor 1.0000 150 1512promotor 1.0000 150 1531promotor 1.0000 150 1547promotor 1.0000 150 1631promotor 1.0000 150 1636promotor 1.0000 150 1648promotor 1.0000 150 1658promotor 1.0000 150 1670promotor 1.0000 150 1695promotor 1.0000 150 1712promotor 1.0000 150 1719promotor 1.0000 150 1723promotor 1.0000 150 1769promotor 1.0000 150 1779promotor 1.0000 150 1790promotor 1.0000 150 1796promotor 1.0000 150 1813promotor 1.0000 150 1827promotor 1.0000 150 1844promotor 1.0000 150 1850promotor 1.0000 150 1851promotor 1.0000 150 1880promotor 1.0000 150 1883promotor 1.0000 150 1932promotor 1.0000 150 1988promotor 1.0000 150 1991promotor 1.0000 150 2025promotor 1.0000 150 2033promotor 1.0000 150 2035promotor 1.0000 150 ******************************************************************************** ******************************************************************************** COMMAND LINE SUMMARY ******************************************************************************** This information can also be useful in the event you wish to report a problem with the MEME software. command: meme promotors-test.fasta -dna -oc . -nostatus -time 14400 -mod zoops -nmotifs 3 -minw 25 -maxw 60 -objfun classic -markov_order 0 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= 25 maxw= 60 nsites: minsites= 2 maxsites= 100 wnsites= 0.8 theta: spmap= uni spfuzz= 0.5 em: prior= dirichlet b= 0.01 maxiter= 50 distance= 1e-05 trim: wg= 11 ws= 1 endgaps= yes data: n= 15000 N= 100 sample: seed= 0 hsfrac= 0 searchsize= 15000 norand= no csites= 1000 Letter frequencies in dataset: A 0.244 C 0.249 G 0.26 T 0.246 Background letter frequencies (from file dataset with add-one prior applied): A 0.244 C 0.249 G 0.26 T 0.246 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF RYDHWRAAAAAADGMCSSVMVCWTW MEME-1 width = 25 sites = 22 llr = 273 E-value = 2.2e-004 ******************************************************************************** -------------------------------------------------------------------------------- Motif RYDHWRAAAAAADGMCSSVMVCWTW MEME-1 Description -------------------------------------------------------------------------------- Simplified A 514445789aaa3131:245324:6 pos.-specific C 1513::::1:::1:5634333511: probability G 3:4::4::::::4823543132:2: matrix T 13235131::::21::2:1:12574 bits 2.0 * 1.8 *** 1.6 **** 1.4 **** Relative 1.2 ****** Entropy 1.0 ****** * (17.9 bits) 0.8 ****** * ** 0.6 * ****** *** *** 0.4 * ********* *** * * *** 0.2 ******************** **** 0.0 ------------------------- Multilevel ACAATAAAAAAAGGCCGCAAGCTTA consensus GTGCAGT A AGCGCCA AGT sequence T T G C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RYDHWRAAAAAADGMCSSVMVCWTW MEME-1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------------------- 353promotor 119 2.37e-12 AGCTTGCCAC ACATTAAAAAAATGCCGCAAGCTTT ATCAATA 797promotor 65 1.64e-09 AACTTTTGCC GTATAAAAAAAAGGCCGGACAGTTA CCTGTCTGGC 1827promotor 14 1.32e-08 GGAAACTACT ACTATGAAAAAACGCGGCCAATATA TGGCTTTTTA 114promotor 109 1.15e-07 CTATCAGTAT CTGCTAAAAAAAGGCCTGTAGCCTT TCGCCGCGCC 1712promotor 49 1.43e-07 AATGTGGCAA CTGTTGAAAAAAGTACGCCACTTTA TGAAAACGGT 875promotor 93 1.78e-07 AGCAAAACGG GCGCATAAAAAAAGCCCCGGCCAGA AGGACGGGGC 611promotor 41 1.99e-07 TGTCAATGAA ACATAAAAAAAAAGCACATCAATTT GCTGATGTGC 458promotor 56 4.47e-07 TGCGCCAAAG GCGATATAAGAAGGCGCGGATCATA GCATAAAGCG 119promotor 70 4.47e-07 TCAAAAATCA GCGTGGTAAAAATGACGGAGCCATA GATTTCTCTG 1658promotor 86 7.17e-07 CGGCTTTATT GTAAAAATAAAAAAACCCGACATTA CGCCGGGTTA 867promotor 89 7.85e-07 TAGCAACAAA ATGACATAAAAAAGCCGGAAGGCGT TTCCGGCAAA 1723promotor 55 1.44e-06 ACAGATTGTT AGAATAAAAAAATGAATCAGCCTGA TCATTAGCAC 1636promotor 59 1.57e-06 CGCCTTTCAA TCGCTATTCAAAGGCGGCAAAGATA CGCTATTTTG 1416promotor 75 1.71e-06 CCGTCAGTCG TCAAAGTAAAAAAACGCGCAATTGT CGCATTTTGC 904promotor 126 2.01e-06 GTTAAAGGCG ACTCTGATAAAATTGCGGGCGTATT 504promotor 14 2.35e-06 TTGCCAATGA ATTCAGAACAAAAGAGTAGCACTTT TCCGTGCAAT 1670promotor 76 2.97e-06 TATTTTTTTC GCCATGAAAAAAGCCCTCCTGATTA ACAGAGAGGG 308promotor 108 3.45e-06 TGTCACCGTA AACCAGTAAAAAGGGCGACCGCTCT TTTATGATGC 242promotor 88 3.45e-06 ACTCTGCCCA ACGATCAAAAAAGGGGCGACCGCCA ACGATCGCCC 462promotor 76 4.30e-06 CATCCACCAT TCAATAAAAACACGACAGGATCTTA CGCGCAATGT 1719promotor 32 4.62e-06 CGTATGCCTG AAATAGAGAAAATGGCCCACTAATT AAAAGTAAAA 85promotor 55 4.96e-06 AACGCGACAT CATCTTTAAAAAAGCAGACAGCAGA TCCTAAGATC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RYDHWRAAAAAADGMCSSVMVCWTW MEME-1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 353promotor 2.4e-12 118_[+1]_7 797promotor 1.6e-09 64_[+1]_61 1827promotor 1.3e-08 13_[+1]_112 114promotor 1.1e-07 108_[+1]_17 1712promotor 1.4e-07 48_[+1]_77 875promotor 1.8e-07 92_[+1]_33 611promotor 2e-07 40_[+1]_85 458promotor 4.5e-07 55_[+1]_70 119promotor 4.5e-07 69_[+1]_56 1658promotor 7.2e-07 85_[+1]_40 867promotor 7.9e-07 88_[+1]_37 1723promotor 1.4e-06 54_[+1]_71 1636promotor 1.6e-06 58_[+1]_67 1416promotor 1.7e-06 74_[+1]_51 904promotor 2e-06 125_[+1] 504promotor 2.4e-06 13_[+1]_112 1670promotor 3e-06 75_[+1]_50 308promotor 3.4e-06 107_[+1]_18 242promotor 3.4e-06 87_[+1]_38 462promotor 4.3e-06 75_[+1]_50 1719promotor 4.6e-06 31_[+1]_94 85promotor 5e-06 54_[+1]_71 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RYDHWRAAAAAADGMCSSVMVCWTW MEME-1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF RYDHWRAAAAAADGMCSSVMVCWTW width=25 seqs=22 353promotor ( 119) ACATTAAAAAAATGCCGCAAGCTTT 1 797promotor ( 65) GTATAAAAAAAAGGCCGGACAGTTA 1 1827promotor ( 14) ACTATGAAAAAACGCGGCCAATATA 1 114promotor ( 109) CTGCTAAAAAAAGGCCTGTAGCCTT 1 1712promotor ( 49) CTGTTGAAAAAAGTACGCCACTTTA 1 875promotor ( 93) GCGCATAAAAAAAGCCCCGGCCAGA 1 611promotor ( 41) ACATAAAAAAAAAGCACATCAATTT 1 458promotor ( 56) GCGATATAAGAAGGCGCGGATCATA 1 119promotor ( 70) GCGTGGTAAAAATGACGGAGCCATA 1 1658promotor ( 86) GTAAAAATAAAAAAACCCGACATTA 1 867promotor ( 89) ATGACATAAAAAAGCCGGAAGGCGT 1 1723promotor ( 55) AGAATAAAAAAATGAATCAGCCTGA 1 1636promotor ( 59) TCGCTATTCAAAGGCGGCAAAGATA 1 1416promotor ( 75) TCAAAGTAAAAAAACGCGCAATTGT 1 904promotor ( 126) ACTCTGATAAAATTGCGGGCGTATT 1 504promotor ( 14) ATTCAGAACAAAAGAGTAGCACTTT 1 1670promotor ( 76) GCCATGAAAAAAGCCCTCCTGATTA 1 308promotor ( 108) AACCAGTAAAAAGGGCGACCGCTCT 1 242promotor ( 88) ACGATCAAAAAAGGGGCGACCGCCA 1 462promotor ( 76) TCAATAAAAACACGACAGGATCTTA 1 1719promotor ( 32) AAATAGAGAAAATGGCCCACTAATT 1 85promotor ( 55) CATCTTTAAAAAAGCAGACAGCAGA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RYDHWRAAAAAADGMCSSVMVCWTW MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 25 n= 12600 bayes= 10.1869 E= 2.2e-004 89 -87 7 -85 -84 113 -251 15 57 -145 48 -44 74 35 -1110 15 57 -245 -251 115 89 -245 65 -143 148 -1110 -1110 37 174 -1110 -251 -85 189 -145 -1110 -1110 197 -1110 -251 -1110 197 -245 -1110 -1110 203 -1110 -1110 -1110 38 -145 48 -11 -143 -245 157 -143 16 113 -52 -1110 -84 124 7 -1110 -242 35 80 -44 -43 71 65 -1110 57 13 7 -143 103 35 -93 -243 16 13 29 -85 -43 87 -52 -44 57 -87 -1110 102 -1110 -145 -20 147 127 -1110 -1110 73 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RYDHWRAAAAAADGMCSSVMVCWTW MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 25 nsites= 22 E= 2.2e-004 0.454545 0.136364 0.272727 0.136364 0.136364 0.545455 0.045455 0.272727 0.363636 0.090909 0.363636 0.181818 0.409091 0.318182 0.000000 0.272727 0.363636 0.045455 0.045455 0.545455 0.454545 0.045455 0.409091 0.090909 0.681818 0.000000 0.000000 0.318182 0.818182 0.000000 0.045455 0.136364 0.909091 0.090909 0.000000 0.000000 0.954545 0.000000 0.045455 0.000000 0.954545 0.045455 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.318182 0.090909 0.363636 0.227273 0.090909 0.045455 0.772727 0.090909 0.272727 0.545455 0.181818 0.000000 0.136364 0.590909 0.272727 0.000000 0.045455 0.318182 0.454545 0.181818 0.181818 0.409091 0.409091 0.000000 0.363636 0.272727 0.272727 0.090909 0.500000 0.318182 0.136364 0.045455 0.272727 0.272727 0.318182 0.136364 0.181818 0.454545 0.181818 0.181818 0.363636 0.136364 0.000000 0.500000 0.000000 0.090909 0.227273 0.681818 0.590909 0.000000 0.000000 0.409091 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RYDHWRAAAAAADGMCSSVMVCWTW MEME-1 regular expression -------------------------------------------------------------------------------- [AG][CT][AG][ACT][TA][AG][AT]AAAAA[GAT]G[CA][CG][GC][CG][ACG][AC][GAC]C[TA][TG][AT] -------------------------------------------------------------------------------- Time 6.78 secs. ******************************************************************************** ******************************************************************************** MOTIF CAKAAWTAATAACNTHTTNTDAHAACHVKCWTAACVATTKDAAYC MEME-2 width = 45 sites = 5 llr = 163 E-value = 3.8e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif CAKAAWTAATAACNTHTTNTDAHAACHVKCWTAACVATTKDAAYC MEME-2 Description -------------------------------------------------------------------------------- Simplified A :8:8a6:8828822:22:422828a244::4266:2822:488:: pos.-specific C a:::::::::2284242:22::4::642:8:::2842:2::::68 probability G ::42::22:2:::2::::2:42:::::442::2::4:::44:::: matrix T :26::48:26:::2846a264:42:22:6:68222::86622242 bits 2.0 * * * * 1.8 * * * * 1.6 * * * * 1.4 * * * * Relative 1.2 ** ** *** *** * * * ** * * * ** ** * Entropy 1.0 ********* *** * * * ** **** * ** * **** (47.0 bits) 0.8 ********* *** * * * ** **** * ** * **** 0.6 ************* * ** * * *** ******* **** **** 0.4 ************* **** ************************** 0.2 ************* **** ************************** 0.0 --------------------------------------------- Multilevel CATAAATAATAACCTCTTATGACAACAATCTTAACCATTTAAACC consensus TGG TGGTACCAACTA CATGTT ACGGGAAGCTGCAAGGTTTT sequence G G AC GCA A TTC TT A C T T T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CAKAAWTAATAACNTHTTNTDAHAACHVKCWTAACVATTKDAAYC MEME-2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------------------------------- 1038promotor 75 3.12e-18 ATGCAGCAGA CATGATTGATAACATCTTGTTATAACAGGCATAACCATTTATACC CGCCAATCTG 2035promotor 68 7.20e-18 GGTTCAGATT CAGAAATAAAAACCTTATAAAACAACAATCTTTACAAATTGAACC AACTGAACCA 540promotor 98 2.28e-15 TAACGTGACA CAGAATTATTAACGCTCTCTGATAAACATCAAGACGATCGGAATC GGCGTCAA 1719promotor 80 7.99e-15 TATTTAATCT CATAAAGAATACCTTCTTTCTAAAATTGGCTTATTCATTGTATTC CTTATCTGCG 1103promotor 53 4.84e-14 TGATTCTTCC CTTAAATAAGCAACTATTATGGCTACCCTGTTACCGCTATAAACT AACCGGACAG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CAKAAWTAATAACNTHTTNTDAHAACHVKCWTAACVATTKDAAYC MEME-2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 1038promotor 3.1e-18 74_[+2]_31 2035promotor 7.2e-18 67_[+2]_38 540promotor 2.3e-15 97_[+2]_8 1719promotor 8e-15 79_[+2]_26 1103promotor 4.8e-14 52_[+2]_53 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CAKAAWTAATAACNTHTTNTDAHAACHVKCWTAACVATTKDAAYC MEME-2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF CAKAAWTAATAACNTHTTNTDAHAACHVKCWTAACVATTKDAAYC width=45 seqs=5 1038promotor ( 75) CATGATTGATAACATCTTGTTATAACAGGCATAACCATTTATACC 1 2035promotor ( 68) CAGAAATAAAAACCTTATAAAACAACAATCTTTACAAATTGAACC 1 540promotor ( 98) CAGAATTATTAACGCTCTCTGATAAACATCAAGACGATCGGAATC 1 1719promotor ( 80) CATAAAGAATACCTTCTTTCTAAAATTGGCTTATTCATTGTATTC 1 1103promotor ( 53) CTTAAATAAGCAACTATTATGGCTACCCTGTTACCGCTATAAACT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CAKAAWTAATAACNTHTTNTDAHAACHVKCWTAACVATTKDAAYC MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 45 n= 10600 bayes= 11.9929 E= 3.8e+001 -897 200 -897 -897 171 -897 -897 -30 -897 -897 62 129 171 -897 -38 -897 203 -897 -897 -897 129 -897 -897 70 -897 -897 -38 170 171 -897 -38 -897 171 -897 -897 -30 -29 -897 -38 129 171 -32 -897 -897 171 -32 -897 -897 -29 168 -897 -897 -29 68 -38 -30 -897 -32 -897 170 -29 68 -897 70 -29 -32 -897 129 -897 -897 -897 202 71 -32 -38 -30 -29 -32 -897 129 -29 -897 62 70 171 -897 -38 -897 -29 68 -897 70 171 -897 -897 -30 203 -897 -897 -897 -29 126 -897 -30 71 68 -897 -30 71 -32 62 -897 -897 -897 62 129 -897 168 -38 -897 71 -897 -897 129 -29 -897 -897 170 129 -897 -38 -30 129 -32 -897 -30 -897 168 -897 -30 -29 68 62 -897 171 -32 -897 -897 -29 -897 -897 170 -29 -32 -897 129 -897 -897 62 129 71 -897 62 -30 171 -897 -897 -30 171 -897 -897 -30 -897 126 -897 70 -897 168 -897 -30 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CAKAAWTAATAACNTHTTNTDAHAACHVKCWTAACVATTKDAAYC MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 45 nsites= 5 E= 3.8e+001 0.000000 1.000000 0.000000 0.000000 0.800000 0.000000 0.000000 0.200000 0.000000 0.000000 0.400000 0.600000 0.800000 0.000000 0.200000 0.000000 1.000000 0.000000 0.000000 0.000000 0.600000 0.000000 0.000000 0.400000 0.000000 0.000000 0.200000 0.800000 0.800000 0.000000 0.200000 0.000000 0.800000 0.000000 0.000000 0.200000 0.200000 0.000000 0.200000 0.600000 0.800000 0.200000 0.000000 0.000000 0.800000 0.200000 0.000000 0.000000 0.200000 0.800000 0.000000 0.000000 0.200000 0.400000 0.200000 0.200000 0.000000 0.200000 0.000000 0.800000 0.200000 0.400000 0.000000 0.400000 0.200000 0.200000 0.000000 0.600000 0.000000 0.000000 0.000000 1.000000 0.400000 0.200000 0.200000 0.200000 0.200000 0.200000 0.000000 0.600000 0.200000 0.000000 0.400000 0.400000 0.800000 0.000000 0.200000 0.000000 0.200000 0.400000 0.000000 0.400000 0.800000 0.000000 0.000000 0.200000 1.000000 0.000000 0.000000 0.000000 0.200000 0.600000 0.000000 0.200000 0.400000 0.400000 0.000000 0.200000 0.400000 0.200000 0.400000 0.000000 0.000000 0.000000 0.400000 0.600000 0.000000 0.800000 0.200000 0.000000 0.400000 0.000000 0.000000 0.600000 0.200000 0.000000 0.000000 0.800000 0.600000 0.000000 0.200000 0.200000 0.600000 0.200000 0.000000 0.200000 0.000000 0.800000 0.000000 0.200000 0.200000 0.400000 0.400000 0.000000 0.800000 0.200000 0.000000 0.000000 0.200000 0.000000 0.000000 0.800000 0.200000 0.200000 0.000000 0.600000 0.000000 0.000000 0.400000 0.600000 0.400000 0.000000 0.400000 0.200000 0.800000 0.000000 0.000000 0.200000 0.800000 0.000000 0.000000 0.200000 0.000000 0.600000 0.000000 0.400000 0.000000 0.800000 0.000000 0.200000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CAKAAWTAATAACNTHTTNTDAHAACHVKCWTAACVATTKDAAYC MEME-2 regular expression -------------------------------------------------------------------------------- C[AT][TG][AG]A[AT][TG][AG][AT][TAG][AC][AC][CA][CAGT][TC][CTA][TAC]T[ACGT][TAC][GTA][AG][CTA][AT]A[CAT][ACT][AGC][TG][CG][TA][TA][AGT][ACT][CT][CGA][AC][TA][TAC][TG][AGT][AT][AT][CT][CT] -------------------------------------------------------------------------------- Time 12.76 secs. ******************************************************************************** ******************************************************************************** MOTIF WTAHTCYYRKTTTWKTAMRCTTTTTTKAM MEME-3 width = 29 sites = 7 llr = 147 E-value = 1.0e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif WTAHTCYYRKTTTWKTAMRCTTTTTTKAM MEME-3 Description -------------------------------------------------------------------------------- Simplified A 61631::14:::14::76331::1:::a4 pos.-specific C 1:13:a44113:1:::33:71::11:::6 probability G ::1::::136:1::41::6::::1116:: matrix T 39149:6313797669:11:7aa6794:: bits 2.0 * ** * 1.8 * ** * 1.6 * ** * 1.4 * ** * * ** * * Relative 1.2 * ** ** ** * ** * * Entropy 1.0 * *** ** **** * ** **** (30.4 bits) 0.8 * *** ******* **** ***** 0.6 ** *** ************** ***** 0.4 ******* ******************** 0.2 ***************************** 0.0 ----------------------------- Multilevel ATATTCTCAGTTTTTTAAGCTTTTTTGAC consensus T A CTGTC AG CCAA T A sequence C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif WTAHTCYYRKTTTWKTAMRCTTTTTTKAM MEME-3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ----------------------------- 959promotor 13 5.60e-12 ATTTATTGTT ATATTCTAAGCTAAGTAAGCTTTCTTGAC CCTATTTTGT 1631promotor 70 1.51e-11 CAATGCCCGA TTATTCCGGCTTTTTTACGCCTTTTTGAC GAAATTTGGC 854promotor 23 2.06e-11 GCGGGATAAC ATACTCTTTGTGTAGTAAACTTTTGTGAC CTGCCCTTGC 1779promotor 18 1.01e-10 GTATGGAATA TTGATCCCAGTTTTTTCTTATTTTTTTAA GGTGCAATAG 114promotor 35 2.27e-10 ACCACCCGTG ATATTCCCGGCTTTTGCCGCTTTATGGAA CACACGCTGG 1827promotor 60 5.84e-10 GGATCTTCTC AATCACTTATTTTATTAAGATTTTCTTAA TATTTATCAA 331promotor 5 1.41e-09 GCAT CTCATCTCCTTTCTGTAAACATTGTTTAC CCGATTAGGC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif WTAHTCYYRKTTTWKTAMRCTTTTTTKAM MEME-3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 959promotor 5.6e-12 12_[+3]_109 1631promotor 1.5e-11 69_[+3]_52 854promotor 2.1e-11 22_[+3]_99 1779promotor 1e-10 17_[+3]_104 114promotor 2.3e-10 34_[+3]_87 1827promotor 5.8e-10 59_[+3]_62 331promotor 1.4e-09 4_[+3]_117 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif WTAHTCYYRKTTTWKTAMRCTTTTTTKAM MEME-3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF WTAHTCYYRKTTTWKTAMRCTTTTTTKAM width=29 seqs=7 959promotor ( 13) ATATTCTAAGCTAAGTAAGCTTTCTTGAC 1 1631promotor ( 70) TTATTCCGGCTTTTTTACGCCTTTTTGAC 1 854promotor ( 23) ATACTCTTTGTGTAGTAAACTTTTGTGAC 1 1779promotor ( 18) TTGATCCCAGTTTTTTCTTATTTTTTTAA 1 114promotor ( 35) ATATTCCCGGCTTTTGCCGCTTTATGGAA 1 1827promotor ( 60) AATCACTTATTTTATTAAGATTTTCTTAA 1 331promotor ( 5) CTCATCTCCTTTCTGTAAACATTGTTTAC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif WTAHTCYYRKTTTWKTAMRCTTTTTTKAM MEME-3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 29 n= 12200 bayes= 10.6102 E= 1.0e+002 122 -80 -945 22 -77 -945 -945 180 122 -80 -86 -78 23 20 -945 80 -77 -945 -945 180 -945 200 -945 -945 -945 78 -945 122 -77 78 -86 22 81 -80 13 -78 -945 -80 113 22 -945 20 -945 154 -945 -945 -86 180 -77 -80 -945 154 81 -945 -945 122 -945 -945 72 122 -945 -945 -86 180 155 20 -945 -945 122 20 -945 -78 23 -945 113 -78 23 152 -945 -945 -77 -80 -945 154 -945 -945 -945 202 -945 -945 -945 202 -77 -80 -86 122 -945 -80 -86 154 -945 -945 -86 180 -945 -945 113 80 203 -945 -945 -945 81 119 -945 -945 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif WTAHTCYYRKTTTWKTAMRCTTTTTTKAM MEME-3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 29 nsites= 7 E= 1.0e+002 0.571429 0.142857 0.000000 0.285714 0.142857 0.000000 0.000000 0.857143 0.571429 0.142857 0.142857 0.142857 0.285714 0.285714 0.000000 0.428571 0.142857 0.000000 0.000000 0.857143 0.000000 1.000000 0.000000 0.000000 0.000000 0.428571 0.000000 0.571429 0.142857 0.428571 0.142857 0.285714 0.428571 0.142857 0.285714 0.142857 0.000000 0.142857 0.571429 0.285714 0.000000 0.285714 0.000000 0.714286 0.000000 0.000000 0.142857 0.857143 0.142857 0.142857 0.000000 0.714286 0.428571 0.000000 0.000000 0.571429 0.000000 0.000000 0.428571 0.571429 0.000000 0.000000 0.142857 0.857143 0.714286 0.285714 0.000000 0.000000 0.571429 0.285714 0.000000 0.142857 0.285714 0.000000 0.571429 0.142857 0.285714 0.714286 0.000000 0.000000 0.142857 0.142857 0.000000 0.714286 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.142857 0.142857 0.142857 0.571429 0.000000 0.142857 0.142857 0.714286 0.000000 0.000000 0.142857 0.857143 0.000000 0.000000 0.571429 0.428571 1.000000 0.000000 0.000000 0.000000 0.428571 0.571429 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif WTAHTCYYRKTTTWKTAMRCTTTTTTKAM MEME-3 regular expression -------------------------------------------------------------------------------- [AT]TA[TAC]TC[TC][CT][AG][GT][TC]TT[TA][TG]T[AC][AC][GA][CA]TTTTTT[GT]A[CA] -------------------------------------------------------------------------------- Time 18.65 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 21promotor 1.32e-01 150 85promotor 4.77e-05 54_[+1(4.96e-06)]_71 114promotor 5.86e-11 34_[+3(2.27e-10)]_45_[+1(1.15e-07)]_\ 17 119promotor 1.74e-05 69_[+1(4.47e-07)]_56 142promotor 1.23e-01 150 143promotor 3.61e-01 150 151promotor 4.43e-01 150 170promotor 9.92e-01 150 185promotor 8.12e-01 150 194promotor 9.20e-01 150 240promotor 3.00e-02 150 242promotor 1.40e-02 87_[+1(3.45e-06)]_38 277promotor 1.74e-01 150 287promotor 9.12e-01 150 308promotor 1.28e-04 10_[+3(5.01e-05)]_68_[+1(3.45e-06)]_\ 18 309promotor 1.74e-01 150 331promotor 6.41e-06 4_[+3(1.41e-09)]_117 352promotor 4.01e-01 150 353promotor 3.84e-10 118_[+1(2.37e-12)]_7 421promotor 9.99e-01 150 440promotor 8.82e-01 150 448promotor 7.89e-01 150 458promotor 1.52e-03 55_[+1(4.47e-07)]_70 459promotor 8.64e-01 150 462promotor 7.22e-04 75_[+1(4.30e-06)]_50 496promotor 6.02e-02 150 504promotor 3.82e-04 13_[+1(2.35e-06)]_112 526promotor 6.27e-01 150 530promotor 2.77e-01 150 540promotor 1.19e-11 97_[+2(2.28e-15)]_8 544promotor 7.33e-01 150 549promotor 9.97e-01 150 551promotor 7.00e-02 150 560promotor 5.49e-01 150 597promotor 3.84e-01 150 598promotor 3.79e-01 150 599promotor 7.93e-01 150 611promotor 3.02e-05 40_[+1(1.99e-07)]_85 671promotor 8.80e-01 150 729promotor 9.41e-01 150 752promotor 2.91e-01 150 769promotor 7.21e-04 3_[+2(1.92e-05)]_102 795promotor 2.46e-01 150 797promotor 2.51e-05 64_[+1(1.64e-09)]_61 799promotor 2.36e-01 150 821promotor 2.00e-01 150 831promotor 6.55e-01 150 837promotor 9.37e-01 150 843promotor 9.71e-01 150 854promotor 2.41e-07 22_[+3(2.06e-11)]_99 867promotor 6.74e-06 88_[+1(7.85e-07)]_37 875promotor 1.55e-03 92_[+1(1.78e-07)]_33 900promotor 9.85e-01 150 904promotor 7.46e-04 125_[+1(2.01e-06)] 926promotor 7.06e-01 150 959promotor 2.51e-09 12_[+3(5.60e-12)]_109 985promotor 5.38e-01 150 1038promotor 9.48e-15 74_[+2(3.12e-18)]_31 1048promotor 3.51e-01 150 1074promotor 9.87e-02 150 1099promotor 3.74e-02 150 1103promotor 3.11e-10 52_[+2(4.84e-14)]_53 1109promotor 8.00e-01 150 1139promotor 8.84e-01 150 1205promotor 3.38e-01 150 1254promotor 9.61e-01 150 1265promotor 7.37e-01 150 1273promotor 2.65e-01 150 1404promotor 4.05e-01 150 1416promotor 1.58e-03 74_[+1(1.71e-06)]_51 1508promotor 6.43e-01 150 1512promotor 9.54e-01 150 1531promotor 7.80e-01 150 1547promotor 9.93e-01 150 1631promotor 9.02e-09 69_[+3(1.51e-11)]_52 1636promotor 2.26e-03 58_[+1(1.57e-06)]_67 1648promotor 4.05e-01 150 1658promotor 5.00e-04 85_[+1(7.17e-07)]_40 1670promotor 3.68e-04 75_[+1(2.97e-06)]_50 1695promotor 3.12e-01 150 1712promotor 4.05e-04 48_[+1(1.43e-07)]_77 1719promotor 2.64e-14 31_[+1(4.62e-06)]_23_[+2(7.99e-15)]_\ 26 1723promotor 1.20e-03 54_[+1(1.44e-06)]_71 1769promotor 7.94e-01 150 1779promotor 2.27e-07 17_[+3(1.01e-10)]_104 1790promotor 1.56e-01 150 1796promotor 9.98e-01 150 1813promotor 8.23e-01 150 1827promotor 6.02e-12 13_[+1(1.32e-08)]_21_[+3(5.84e-10)]_\ 62 1844promotor 7.10e-01 150 1850promotor 4.54e-01 150 1851promotor 6.31e-01 150 1880promotor 9.76e-02 150 1883promotor 4.28e-01 150 1932promotor 3.64e-02 150 1988promotor 3.06e-01 150 1991promotor 8.83e-01 150 2025promotor 9.60e-01 150 2033promotor 1.68e-01 150 2035promotor 2.30e-15 67_[+2(7.20e-18)]_38 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (3) found. ******************************************************************************** CPU: noble-meme.grid.gs.washington.edu ********************************************************************************