******************************************************************************** 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.fasta CONTROL SEQUENCES= --none-- ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ Operon2261 1.0000 150 Operon638 1.0000 150 Operon2128 1.0000 150 Operon2877 1.0000 150 Operon1460 1.0000 150 Operon2586 1.0000 150 Operon2170 1.0000 150 Operon1050 1.0000 150 Operon2245 1.0000 150 Operon1017 1.0000 150 Operon105 1.0000 150 Operon1970 1.0000 150 Operon684 1.0000 150 Operon1277 1.0000 150 Operon2716 1.0000 150 Operon1261 1.0000 150 Operon496 1.0000 150 Operon1655 1.0000 150 Operon706 1.0000 150 Operon2028 1.0000 150 Operon2123 1.0000 150 Operon602 1.0000 150 Operon2430 1.0000 150 Operon136 1.0000 150 Operon1632 1.0000 150 Operon2023 1.0000 150 Operon2036 1.0000 150 Operon2588 1.0000 150 Operon2755 1.0000 150 Operon1419 1.0000 150 Operon1208 1.0000 150 Operon1459 1.0000 150 Operon1410 1.0000 150 Operon2335 1.0000 150 Operon1609 1.0000 150 Operon1611 1.0000 150 Operon2732 1.0000 150 Operon649 1.0000 150 Operon866 1.0000 150 Operon251 1.0000 150 Operon2553 1.0000 150 Operon1133 1.0000 150 Operon1465 1.0000 150 Operon2628 1.0000 150 Operon2008 1.0000 150 Operon2872 1.0000 150 Operon2861 1.0000 150 Operon2651 1.0000 150 Operon2954 1.0000 150 Operon1185 1.0000 150 Operon197 1.0000 150 Operon2969 1.0000 150 Operon1902 1.0000 150 Operon1757 1.0000 150 Operon1686 1.0000 150 Operon2000 1.0000 150 Operon2188 1.0000 150 Operon1069 1.0000 150 Operon2251 1.0000 150 Operon2756 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 Train.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= 60 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= 9000 N= 60 sample: seed= 0 hsfrac= 0 searchsize= 9000 norand= no csites= 1000 Letter frequencies in dataset: A 0.193 C 0.32 G 0.303 T 0.185 Background letter frequencies (from file dataset with add-one prior applied): A 0.193 C 0.32 G 0.303 T 0.185 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF WYMAWYGHTHRNHNRRAAYDHTHKTWMMBTTDTCGAW MEME-1 width = 37 sites = 11 llr = 217 E-value = 1.7e-003 ******************************************************************************** -------------------------------------------------------------------------------- Motif WYMAWYGHTHRNHNRRAAYDHTHKTWMMBTTDTCGAW MEME-1 Description -------------------------------------------------------------------------------- Simplified A 4:56512433333234672451322455:1342:193 pos.-specific C :531:423:32233212:313:3:2:543111:7::2 probability G ::1:2:5:1:5312551:13:3132:::31:3::9:: matrix T 65134514651344::135336455612576383:15 bits 2.4 2.2 1.9 * 1.7 * * Relative 1.5 * * * * ** Entropy 1.2 * * * * * * ** (28.5 bits) 1.0 ** * * * * * ** **** 0.7 ** *** *** *** ** * *** ** ***** 0.5 ****** *** **** ** * ****** ***** 0.2 *********** ************************* 0.0 ------------------------------------- Multilevel TCAAATGATTGATTGGAATAATTTTTAATTTATCGAT consensus ATCTTC TAAAGACAA TCGCGAG ACCC AG T A sequence C C TC TT C G T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif WYMAWYGHTHRNHNRRAAYDHTHKTWMMBTTDTCGAW MEME-1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------------------------------- Operon684 7 2.99e-14 ATTGCC TTACATGATTGCTAGGAATTTTCTGTAAGTTTTCGAT GTGCTCGAGC Operon1611 40 8.32e-14 CAATAACGTC ACATTTGAAAGTTTCGATTAAGTTTTCCGTTATCGAT TATCCATAAA Operon1277 35 3.76e-13 GAAACAAGGC TTTAAAGCTTGATGAGAATTATTATAAATTTAATGAT TTCATACTGC Operon1609 33 1.54e-10 CATCCTGACC TCCATTATTTGTATCGATCACTATAAATTTACTTGAC GAGCGTTGCC Operon496 42 1.86e-10 CGTCGGGCTG TCAATCGATTTTTCGAAAAAAGTGTTTTTTCTTCAAA TGCTTAGCGC Operon2628 24 1.14e-09 TAACTTACTG ATAAATAATAAGAAAACACATAATCACCCATGTCGAT AGACACTATC Operon2969 59 1.98e-09 CATCAAGCGG TTCAGCGTACGCATGGTAACCTTGCTCCTTTATCGAA TCGTCCAGGG Operon2430 35 2.69e-09 TCGATGAGAG TCAAACTTAAAACGGACAGGATGTGACATTTTTTGAC AGCTGGATTT Operon1133 80 7.36e-09 TGCTGCGGCG TCCTTTCTTCAGCTACATTTTTCTTTCAGCAGTCGTT CCCATCATCC Operon2036 81 8.44e-09 TGCTGGCGGA ATATATCCGTCAGCGGGACGATAGTTAACGTATCGAT GGCTGGCCGA Operon866 99 8.61e-08 GTGGGGCGCC ACGAGCGCTCCGCCGAAATGCGCAATACCTAGACGAA TAACGGTAGA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif WYMAWYGHTHRNHNRRAAYDHTHKTWMMBTTDTCGAW MEME-1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- Operon684 3e-14 6_[+1]_107 Operon1611 8.3e-14 39_[+1]_74 Operon1277 3.8e-13 34_[+1]_79 Operon1609 1.5e-10 32_[+1]_81 Operon496 1.9e-10 41_[+1]_72 Operon2628 1.1e-09 23_[+1]_90 Operon2969 2e-09 58_[+1]_55 Operon2430 2.7e-09 34_[+1]_79 Operon1133 7.4e-09 79_[+1]_34 Operon2036 8.4e-09 80_[+1]_33 Operon866 8.6e-08 98_[+1]_15 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif WYMAWYGHTHRNHNRRAAYDHTHKTWMMBTTDTCGAW MEME-1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF WYMAWYGHTHRNHNRRAAYDHTHKTWMMBTTDTCGAW width=37 seqs=11 Operon684 ( 7) TTACATGATTGCTAGGAATTTTCTGTAAGTTTTCGAT 1 Operon1611 ( 40) ACATTTGAAAGTTTCGATTAAGTTTTCCGTTATCGAT 1 Operon1277 ( 35) TTTAAAGCTTGATGAGAATTATTATAAATTTAATGAT 1 Operon1609 ( 33) TCCATTATTTGTATCGATCACTATAAATTTACTTGAC 1 Operon496 ( 42) TCAATCGATTTTTCGAAAAAAGTGTTTTTTCTTCAAA 1 Operon2628 ( 24) ATAAATAATAAGAAAACACATAATCACCCATGTCGAT 1 Operon2969 ( 59) TTCAGCGTACGCATGGTAACCTTGCTCCTTTATCGAA 1 Operon2430 ( 35) TCAAACTTAAAACGGACAGGATGTGACATTTTTTGAC 1 Operon1133 ( 80) TCCTTTCTTCAGCTACATTTTTCTTTCAGCAGTCGTT 1 Operon2036 ( 81) ATATATCCGTCAGCGGGACGATAGTTAACGTATCGAT 1 Operon866 ( 99) ACGAGCGCTCCGCCGAAATGCGCAATACCTAGACGAA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif WYMAWYGHTHRNHNRRAAYDHTHKTWMMBTTDTCGAW MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 37 n= 6840 bayes= 10.3057 E= 1.7e-003 91 -1010 -1010 178 -1010 77 -1010 130 150 -23 -173 -102 172 -181 -1010 56 123 -1010 -73 97 -108 19 -1010 156 -9 -81 85 -102 91 -23 -1010 97 50 -1010 -173 178 50 -23 -1010 130 50 -81 59 -102 50 -81 -15 56 50 -23 -173 97 -9 -23 -73 97 50 -81 85 -1010 91 -181 85 -1010 172 -81 -173 -102 191 -1010 -1010 56 -9 -23 -173 130 91 -181 -15 56 123 -23 -1010 56 -108 -1010 -15 178 50 -23 -173 97 -9 -1010 -15 156 -9 -81 -73 130 91 -1010 -1010 178 123 51 -1010 -102 123 19 -1010 -2 -1010 -23 -15 130 -108 -181 -173 197 50 -181 -1010 178 91 -181 -15 56 -9 -1010 -1010 214 -1010 119 -1010 56 -108 -1010 159 -1010 223 -1010 -1010 -102 50 -81 -1010 156 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif WYMAWYGHTHRNHNRRAAYDHTHKTWMMBTTDTCGAW MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 37 nsites= 11 E= 1.7e-003 0.363636 0.000000 0.000000 0.636364 0.000000 0.545455 0.000000 0.454545 0.545455 0.272727 0.090909 0.090909 0.636364 0.090909 0.000000 0.272727 0.454545 0.000000 0.181818 0.363636 0.090909 0.363636 0.000000 0.545455 0.181818 0.181818 0.545455 0.090909 0.363636 0.272727 0.000000 0.363636 0.272727 0.000000 0.090909 0.636364 0.272727 0.272727 0.000000 0.454545 0.272727 0.181818 0.454545 0.090909 0.272727 0.181818 0.272727 0.272727 0.272727 0.272727 0.090909 0.363636 0.181818 0.272727 0.181818 0.363636 0.272727 0.181818 0.545455 0.000000 0.363636 0.090909 0.545455 0.000000 0.636364 0.181818 0.090909 0.090909 0.727273 0.000000 0.000000 0.272727 0.181818 0.272727 0.090909 0.454545 0.363636 0.090909 0.272727 0.272727 0.454545 0.272727 0.000000 0.272727 0.090909 0.000000 0.272727 0.636364 0.272727 0.272727 0.090909 0.363636 0.181818 0.000000 0.272727 0.545455 0.181818 0.181818 0.181818 0.454545 0.363636 0.000000 0.000000 0.636364 0.454545 0.454545 0.000000 0.090909 0.454545 0.363636 0.000000 0.181818 0.000000 0.272727 0.272727 0.454545 0.090909 0.090909 0.090909 0.727273 0.272727 0.090909 0.000000 0.636364 0.363636 0.090909 0.272727 0.272727 0.181818 0.000000 0.000000 0.818182 0.000000 0.727273 0.000000 0.272727 0.090909 0.000000 0.909091 0.000000 0.909091 0.000000 0.000000 0.090909 0.272727 0.181818 0.000000 0.545455 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif WYMAWYGHTHRNHNRRAAYDHTHKTWMMBTTDTCGAW MEME-1 regular expression -------------------------------------------------------------------------------- [TA][CT][AC][AT][AT][TC]G[ATC][TA][TAC][GA][AGT][TAC][TC][GA][GA]A[AT][TC][AGT][ACT][TG][TAC][TG]T[TA][AC][AC][TCG]T[TA][AGT]T[CT]GA[TA] -------------------------------------------------------------------------------- Time 5.42 secs. ******************************************************************************** ******************************************************************************** MOTIF ACKMCAAGMSYSNCNKSGMGKCCTKCC MEME-2 width = 27 sites = 6 llr = 125 E-value = 1.6e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif ACKMCAAGMSYSNCNKSGMGKCCTKCC MEME-2 Description -------------------------------------------------------------------------------- Simplified A 7::5:88:5:::3:3:::7:::2:::: pos.-specific C 28:3a:::3773283:5:3:288:2aa probability G ::5::::a:3:73:275a:a32:23:: matrix T 2252:22:2:3:2223::::5::85:: bits 2.4 2.2 1.9 1.7 **** * * * ** Relative 1.5 **** * * * ** Entropy 1.2 * **** * *** ** ** (30.0 bits) 1.0 *** **** * * * *** *** ** 0.7 ************ * ***** *** ** 0.5 ************ * ************ 0.2 ************** ************ 0.0 --------------------------- Multilevel ACGACAAGACCGACAGCGAGTCCTTCC consensus TC CGTCG CTG C G G sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ACKMCAAGMSYSNCNKSGMGKCCTKCC MEME-2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------------- Operon2023 123 1.87e-12 GTGAGCACTT ATTCCAAGACCGACCGGGAGTCCTGCC A Operon2188 93 2.37e-11 CTCCAGGCTT ACGACAAGCGCGACAGCGCGTCCTCCC CTAATAAGCA Operon1050 103 2.33e-10 TCTATGAATG ACTTCAAGTCCGCCCTGGCGCCCTTCC CGCCCGACTA Operon2872 77 3.71e-10 ATGCGTATCA TCGACAAGCGTGGCATCGAGGCCGTCC TGGCTGACCT Operon2954 122 5.72e-10 CCGGTGCTGA CCTACAAGACCCGTGGGGAGTGCTGCC GA Operon1611 123 1.16e-09 CATAGATTGC ACGCCTTGACTCTCTGCGAGGCATTCC C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ACKMCAAGMSYSNCNKSGMGKCCTKCC MEME-2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- Operon2023 1.9e-12 122_[+2]_1 Operon2188 2.4e-11 92_[+2]_31 Operon1050 2.3e-10 102_[+2]_21 Operon2872 3.7e-10 76_[+2]_47 Operon2954 5.7e-10 121_[+2]_2 Operon1611 1.2e-09 122_[+2]_1 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ACKMCAAGMSYSNCNKSGMGKCCTKCC MEME-2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF ACKMCAAGMSYSNCNKSGMGKCCTKCC width=27 seqs=6 Operon2023 ( 123) ATTCCAAGACCGACCGGGAGTCCTGCC 1 Operon2188 ( 93) ACGACAAGCGCGACAGCGCGTCCTCCC 1 Operon1050 ( 103) ACTTCAAGTCCGCCCTGGCGCCCTTCC 1 Operon2872 ( 77) TCGACAAGCGTGGCATCGAGGCCGTCC 1 Operon2954 ( 122) CCTACAAGACCCGTGGGGAGTGCTGCC 1 Operon1611 ( 123) ACGCCTTGACTCTCTGCGAGGCATTCC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ACKMCAAGMSYSNCNKSGMGKCCTKCC MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 27 n= 7440 bayes= 10.7227 E= 1.6e+002 179 -94 -923 -15 -923 138 -923 -15 -923 -923 72 143 137 6 -923 -15 -923 164 -923 -923 211 -923 -923 -15 211 -923 -923 -15 -923 -923 172 -923 137 6 -923 -15 -923 106 14 -923 -923 106 -923 85 -923 6 114 -923 79 -94 14 -15 -923 138 -923 -15 79 6 -86 -15 -923 -923 114 85 -923 65 72 -923 -923 -923 172 -923 179 6 -923 -923 -923 -923 172 -923 -923 -94 14 143 -923 138 -86 -923 -21 138 -923 -923 -923 -923 -86 217 -923 -94 14 143 -923 164 -923 -923 -923 164 -923 -923 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ACKMCAAGMSYSNCNKSGMGKCCTKCC MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 27 nsites= 6 E= 1.6e+002 0.666667 0.166667 0.000000 0.166667 0.000000 0.833333 0.000000 0.166667 0.000000 0.000000 0.500000 0.500000 0.500000 0.333333 0.000000 0.166667 0.000000 1.000000 0.000000 0.000000 0.833333 0.000000 0.000000 0.166667 0.833333 0.000000 0.000000 0.166667 0.000000 0.000000 1.000000 0.000000 0.500000 0.333333 0.000000 0.166667 0.000000 0.666667 0.333333 0.000000 0.000000 0.666667 0.000000 0.333333 0.000000 0.333333 0.666667 0.000000 0.333333 0.166667 0.333333 0.166667 0.000000 0.833333 0.000000 0.166667 0.333333 0.333333 0.166667 0.166667 0.000000 0.000000 0.666667 0.333333 0.000000 0.500000 0.500000 0.000000 0.000000 0.000000 1.000000 0.000000 0.666667 0.333333 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.166667 0.333333 0.500000 0.000000 0.833333 0.166667 0.000000 0.166667 0.833333 0.000000 0.000000 0.000000 0.000000 0.166667 0.833333 0.000000 0.166667 0.333333 0.500000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ACKMCAAGMSYSNCNKSGMGKCCTKCC MEME-2 regular expression -------------------------------------------------------------------------------- AC[GT][AC]CAAG[AC][CG][CT][GC][AG]C[AC][GT][CG]G[AC]G[TG]CCT[TG]CC -------------------------------------------------------------------------------- Time 10.56 secs. ******************************************************************************** ******************************************************************************** MOTIF YCGASSCGSYRKTC MEME-3 width = 14 sites = 22 llr = 202 E-value = 6.1e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif YCGASSCGSYRKTC MEME-3 Description -------------------------------------------------------------------------------- Simplified A :2281:1:1:4::: pos.-specific C 46::368:34:::9 probability G :27:53:a5:55:1 matrix T 5::221:::614a: bits 2.4 * 2.2 * 1.9 * 1.7 * * Relative 1.5 * * * Entropy 1.2 * * * ** (13.3 bits) 1.0 ** ** * ** 0.7 * ** ** ***** 0.5 **** ********* 0.2 **** ********* 0.0 -------------- Multilevel TCGAGCCGGTGGTC consensus CGA CG CCAT sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif YCGASSCGSYRKTC MEME-3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------------- Operon649 20 2.31e-07 CCCGGCGAGG TCGAGGCGGTGGTC GAGGTCGGGA Operon2128 103 2.11e-06 CGGCGGAGCG CCGACCCGGCATTC CGTCGCCAGG Operon1686 131 2.90e-06 CAGCAGGCCT TGGAACCGGTAGTC CAGACA Operon2954 50 3.41e-06 TACAAGGGTA TCGACTCGGTGGTC GGCGCGCTGC Operon638 57 3.97e-06 CAACAGGACG TAAAGCCGCTGGTC GACAACCGCT Operon2251 78 5.14e-06 CCCGAACCGC CCGAGGCGGCGGTC CGGTGAACTC Operon251 50 8.59e-06 CGCTCGCCGC TGGAGTCGCTGTTC GGCGGCGGCA Operon2586 101 1.47e-05 CAGCTCGACG ACGAGCCGGCGTTC CTCGCCCAGT Operon684 48 2.20e-05 TTCGATGTGC TCGAGCCGGTTGTG CCGTTTTCGG Operon2588 35 2.63e-05 GAGCACCTAT CCGATCAGCCAGTC CGCCGGCTTG Operon1185 94 2.89e-05 ACCGCCACCA CGGACCCGCCGGTC TCCTTGCCAC Operon2732 83 3.14e-05 CCGGGGATAG TCGATGCGCTGGTG CGCGCCACCA Operon197 92 3.75e-05 CGATGCGGCA CAATTCCGCTATTC CCGTTACCGA Operon1465 107 3.75e-05 GCCCCGGAAC TCGTAGCGGTTTTC GTCGCCTCCG Operon706 137 3.75e-05 CCGCACTTGA CCAAGGAGATGTTC Operon2755 100 4.06e-05 AGCCTGATAA TGTTGCCGGTATTC GGAGGTATCT Operon1757 15 5.16e-05 AGTTGGCCGG CCAACGCGACGGTC GCCAGCAGGG Operon136 111 5.59e-05 GTAGTCGAGG TAGACCCGCTGCTC ACGGCATTCC Operon2651 91 6.04e-05 AACTCGGTGC CCGATCGGGCAGTC TGCTCTTTCA Operon602 4 6.50e-05 GGT GAAAGCCGGCATTC CAGGGCTCCT Operon2861 100 7.55e-05 ACCTGTTCCA TCGACGCCGCAGTC GATCACTTGC Operon1017 12 7.55e-05 CGCGTGGTCT CGGTGCAGATATTC GATCACGTCG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif YCGASSCGSYRKTC MEME-3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- Operon649 2.3e-07 19_[+3]_117 Operon2128 2.1e-06 102_[+3]_34 Operon1686 2.9e-06 130_[+3]_6 Operon2954 3.4e-06 49_[+3]_87 Operon638 4e-06 56_[+3]_80 Operon2251 5.1e-06 77_[+3]_59 Operon251 8.6e-06 49_[+3]_87 Operon2586 1.5e-05 100_[+3]_36 Operon684 2.2e-05 47_[+3]_89 Operon2588 2.6e-05 34_[+3]_102 Operon1185 2.9e-05 93_[+3]_43 Operon2732 3.1e-05 82_[+3]_54 Operon197 3.7e-05 91_[+3]_45 Operon1465 3.7e-05 106_[+3]_30 Operon706 3.7e-05 136_[+3] Operon2755 4.1e-05 99_[+3]_37 Operon1757 5.2e-05 14_[+3]_122 Operon136 5.6e-05 110_[+3]_26 Operon2651 6e-05 90_[+3]_46 Operon602 6.5e-05 3_[+3]_133 Operon2861 7.5e-05 99_[+3]_37 Operon1017 7.5e-05 11_[+3]_125 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif YCGASSCGSYRKTC MEME-3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF YCGASSCGSYRKTC width=14 seqs=22 Operon649 ( 20) TCGAGGCGGTGGTC 1 Operon2128 ( 103) CCGACCCGGCATTC 1 Operon1686 ( 131) TGGAACCGGTAGTC 1 Operon2954 ( 50) TCGACTCGGTGGTC 1 Operon638 ( 57) TAAAGCCGCTGGTC 1 Operon2251 ( 78) CCGAGGCGGCGGTC 1 Operon251 ( 50) TGGAGTCGCTGTTC 1 Operon2586 ( 101) ACGAGCCGGCGTTC 1 Operon684 ( 48) TCGAGCCGGTTGTG 1 Operon2588 ( 35) CCGATCAGCCAGTC 1 Operon1185 ( 94) CGGACCCGCCGGTC 1 Operon2732 ( 83) TCGATGCGCTGGTG 1 Operon197 ( 92) CAATTCCGCTATTC 1 Operon1465 ( 107) TCGTAGCGGTTTTC 1 Operon706 ( 137) CCAAGGAGATGTTC 1 Operon2755 ( 100) TGTTGCCGGTATTC 1 Operon1757 ( 15) CCAACGCGACGGTC 1 Operon136 ( 111) TAGACCCGCTGCTC 1 Operon2651 ( 91) CCGATCGGGCAGTC 1 Operon602 ( 4) GAAAGCCGGCATTC 1 Operon2861 ( 100) TCGACGCCGCAGTC 1 Operon1017 ( 12) CGGTGCAGATATTC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif YCGASSCGSYRKTC MEME-3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 14 n= 8220 bayes= 8.89756 E= 6.1e+002 -208 36 -273 143 -9 89 -41 -1110 24 -1110 127 -202 208 -1110 -1110 -2 -109 -23 59 -2 -1110 89 7 -102 -50 136 -273 -1110 -1110 -281 166 -1110 -50 -1 85 -1110 -1110 36 -1110 168 108 -1110 72 -102 -1110 -281 85 115 -1110 -1110 -1110 243 -1110 151 -173 -1110 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif YCGASSCGSYRKTC MEME-3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 14 nsites= 22 E= 6.1e+002 0.045455 0.409091 0.045455 0.500000 0.181818 0.590909 0.227273 0.000000 0.227273 0.000000 0.727273 0.045455 0.818182 0.000000 0.000000 0.181818 0.090909 0.272727 0.454545 0.181818 0.000000 0.590909 0.318182 0.090909 0.136364 0.818182 0.045455 0.000000 0.000000 0.045455 0.954545 0.000000 0.136364 0.318182 0.545455 0.000000 0.000000 0.409091 0.000000 0.590909 0.409091 0.000000 0.500000 0.090909 0.000000 0.045455 0.545455 0.409091 0.000000 0.000000 0.000000 1.000000 0.000000 0.909091 0.090909 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif YCGASSCGSYRKTC MEME-3 regular expression -------------------------------------------------------------------------------- [TC][CG][GA]A[GC][CG]CG[GC][TC][GA][GT]TC -------------------------------------------------------------------------------- Time 15.42 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- Operon2261 1.86e-01 150 Operon638 6.31e-03 56_[+3(3.97e-06)]_80 Operon2128 5.65e-03 102_[+3(2.11e-06)]_34 Operon2877 7.77e-01 150 Operon1460 7.38e-02 150 Operon2586 2.42e-03 100_[+3(1.47e-05)]_36 Operon2170 7.11e-01 150 Operon1050 3.80e-06 102_[+2(2.33e-10)]_21 Operon2245 7.23e-01 150 Operon1017 1.31e-02 11_[+3(7.55e-05)]_125 Operon105 6.23e-01 150 Operon1970 8.96e-01 150 Operon684 1.10e-12 6_[+1(2.99e-14)]_4_[+3(2.20e-05)]_\ 89 Operon1277 1.61e-09 34_[+1(3.76e-13)]_79 Operon2716 8.99e-01 150 Operon1261 7.44e-01 150 Operon496 2.63e-06 41_[+1(1.86e-10)]_72 Operon1655 6.89e-01 150 Operon706 2.27e-02 136_[+3(3.75e-05)] Operon2028 1.92e-01 150 Operon2123 6.45e-01 150 Operon602 1.44e-02 3_[+3(6.50e-05)]_133 Operon2430 2.38e-07 34_[+1(2.69e-09)]_50_[+2(6.15e-05)]_\ 2 Operon136 9.59e-03 110_[+3(5.59e-05)]_26 Operon1632 4.73e-01 150 Operon2023 2.30e-08 122_[+2(1.87e-12)]_1 Operon2036 2.58e-05 80_[+1(8.44e-09)]_33 Operon2588 4.34e-02 34_[+3(2.63e-05)]_102 Operon2755 1.97e-02 99_[+3(4.06e-05)]_37 Operon1419 6.14e-01 150 Operon1208 6.42e-01 150 Operon1459 9.28e-01 150 Operon1410 9.69e-01 150 Operon2335 7.86e-01 150 Operon1609 1.25e-07 32_[+1(1.54e-10)]_81 Operon1611 3.19e-16 39_[+1(8.32e-14)]_46_[+2(1.16e-09)]_\ 1 Operon2732 6.84e-02 82_[+3(3.14e-05)]_54 Operon649 9.64e-05 19_[+3(2.31e-07)]_117 Operon866 2.58e-04 98_[+1(8.61e-08)]_15 Operon251 2.64e-02 49_[+3(8.59e-06)]_87 Operon2553 6.39e-01 150 Operon1133 9.01e-06 79_[+1(7.36e-09)]_34 Operon1465 7.66e-02 106_[+3(3.75e-05)]_30 Operon2628 7.26e-06 23_[+1(1.14e-09)]_17_[+1(3.60e-05)]_\ 36 Operon2008 1.91e-01 150 Operon2872 2.25e-06 76_[+2(3.71e-10)]_47 Operon2861 1.15e-01 99_[+3(7.55e-05)]_37 Operon2651 4.97e-03 90_[+3(6.04e-05)]_46 Operon2954 5.67e-09 49_[+3(3.41e-06)]_58_[+2(5.72e-10)]_\ 2 Operon1185 1.48e-02 93_[+3(2.89e-05)]_43 Operon197 3.25e-02 91_[+3(3.75e-05)]_45 Operon2969 1.19e-05 58_[+1(1.98e-09)]_55 Operon1902 4.44e-01 150 Operon1757 6.46e-02 14_[+3(5.16e-05)]_122 Operon1686 8.97e-04 130_[+3(2.90e-06)]_6 Operon2000 7.24e-01 150 Operon2188 2.77e-07 92_[+2(2.37e-11)]_31 Operon1069 7.69e-02 150 Operon2251 2.98e-03 77_[+3(5.14e-06)]_59 Operon2756 6.83e-01 150 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (3) found. ******************************************************************************** CPU: kodomo ********************************************************************************