******************************************************************************** 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 ------------- ------ ------ ------------- ------ ------ promoter_1 1.0000 150 promoter_2 1.0000 150 promoter_3 1.0000 150 promoter_4 1.0000 150 promoter_5 1.0000 150 promoter_6 1.0000 150 promoter_7 1.0000 150 promoter_8 1.0000 150 promoter_9 1.0000 150 promoter_10 1.0000 150 promoter_11 1.0000 150 promoter_12 1.0000 150 promoter_13 1.0000 150 promoter_14 1.0000 150 promoter_15 1.0000 150 promoter_16 1.0000 150 promoter_17 1.0000 150 promoter_18 1.0000 150 promoter_19 1.0000 150 promoter_20 1.0000 150 promoter_21 1.0000 150 promoter_22 1.0000 150 promoter_23 1.0000 150 promoter_24 1.0000 150 promoter_25 1.0000 150 promoter_26 1.0000 150 promoter_27 1.0000 150 promoter_28 1.0000 150 promoter_29 1.0000 150 promoter_30 1.0000 150 promoter_31 1.0000 150 promoter_32 1.0000 150 promoter_33 1.0000 150 promoter_34 1.0000 150 promoter_35 1.0000 150 promoter_36 1.0000 150 promoter_37 1.0000 150 promoter_38 1.0000 150 promoter_39 1.0000 150 promoter_40 1.0000 150 promoter_41 1.0000 150 promoter_42 1.0000 150 promoter_43 1.0000 150 promoter_44 1.0000 150 promoter_45 1.0000 150 promoter_46 1.0000 150 promoter_47 1.0000 150 promoter_48 1.0000 150 promoter_49 1.0000 150 promoter_50 1.0000 150 promoter_51 1.0000 150 promoter_52 1.0000 150 promoter_53 1.0000 150 promoter_54 1.0000 150 promoter_55 1.0000 150 promoter_56 1.0000 150 promoter_57 1.0000 150 promoter_58 1.0000 150 promoter_59 1.0000 150 promoter_60 1.0000 150 promoter_61 1.0000 150 promoter_62 1.0000 150 promoter_63 1.0000 150 promoter_64 1.0000 150 promoter_65 1.0000 150 promoter_66 1.0000 150 promoter_67 1.0000 150 promoter_68 1.0000 150 promoter_69 1.0000 150 promoter_70 1.0000 150 promoter_71 1.0000 150 promoter_72 1.0000 150 promoter_73 1.0000 150 promoter_74 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 housekeeping.fasta -dna -oc . -nostatus -time 14400 -mod zoops -nmotifs 3 -minw 8 -maxw 50 -objfun classic -minsites 10 -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= 8 maxw= 50 nsites: minsites= 10 maxsites= 74 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= 11100 N= 74 sample: seed= 0 hsfrac= 0 searchsize= 11100 norand= no csites= 1000 Letter frequencies in dataset: A 0.271 C 0.226 G 0.227 T 0.276 Background letter frequencies (from file dataset with add-one prior applied): A 0.271 C 0.226 G 0.227 T 0.276 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF CWGNYGCBTTTTTTB MEME-1 width = 15 sites = 38 llr = 312 E-value = 9.4e-001 ******************************************************************************** -------------------------------------------------------------------------------- Motif CWGNYGCBTTTTTTB MEME-1 Description -------------------------------------------------------------------------------- Simplified A :3:2:1:11::2111 pos.-specific C 82126164::2:134 probability G :19217322:::2:4 matrix T 25:342137a88662 bits 2.1 1.9 1.7 * * 1.5 * * Relative 1.3 * ** Entropy 1.1 * * *** (11.9 bits) 0.9 * * * * **** 0.6 * * *** **** * 0.4 * * *** ****** 0.2 *** *********** 0.0 --------------- Multilevel CTGTCGCCTTTTTTC consensus A AT GTG AGCG sequence C G T G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CWGNYGCBTTTTTTB MEME-1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------- promoter_14 15 1.73e-07 GAGATCTTCT CTGCCGCTTTTTTTT TCATCAATCA promoter_72 30 7.89e-07 TGCACAGACA CTGGCGCTTTTTGTT TATCCAGCTC promoter_31 49 1.31e-06 TCCAGTATAA TAGCCGCCTTTTTTC ATTCAGTTGT promoter_36 21 2.44e-06 TTCGTTCATC CCGACTCCTTTTTTG TATAGATAAA promoter_2 86 3.78e-06 CGGATCCTAC CTGACGCTTTTTATC GCAACTCTCT promoter_40 125 8.40e-06 GTTTGATAGC CAGCCCCCTTTATTG CCGAGGACAT promoter_24 108 8.40e-06 AGCCGCCAGC CAGGCGGCTTTTTTA ACAACTGCAT promoter_3 60 8.40e-06 CCAGGTGAAC CAGTCGTTTTTTTTT GAATTTTATA promoter_61 101 9.52e-06 GGCTATGCTA TTGGCGCGTTCTTTG CCGGCATATT promoter_74 89 1.08e-05 CACTGCATAA CTGTCGGTGTTATCG ACATTACGCG promoter_69 34 1.54e-05 GAACACTTCG CCGCGGCGTTTTTTC ATCATTTCAG promoter_60 115 1.54e-05 GGTGCTCTTG CTGGCGGTGTTATCG GTGGTCTTGG promoter_35 66 1.54e-05 AGAGCCTGCG CTGATGCCGTTTCCC TGAGTGAGGG promoter_53 10 1.93e-05 CAAGGCACA TTGATGCCTTTATCG CCGTCGGAGC promoter_63 62 2.69e-05 GGCCCAAAAA CTGATTGGTTTTGTC TGAAGCCCGT promoter_37 87 2.99e-05 AAGCGCAAGA TTGTTGGTTTTTGCG TGATGGTGGC promoter_25 83 4.09e-05 AAACACCCTC CTGGTACGTTTTGCG TTCGCAGTGG promoter_18 57 5.50e-05 AGAGCATGCG CTGATGCCGTTTCAC TGAAAGTGCA promoter_15 76 6.05e-05 CACAGAAAAG CACTCCCCTTTTGTG CGGTCAGCTT promoter_20 101 6.66e-05 CAACCACAGG CTGCCTTTTTCTTTG ACTCTATGAC promoter_17 1 6.66e-05 . CGGCTCCCTTTTTTT ACCTTTAATT promoter_49 126 7.31e-05 GCATGGGATG ATGATGCCGTTTTTC AGGGGGCAGG promoter_44 125 7.31e-05 TGCTGAATTG TTGACGCATTTATTT ATTGGTATCG promoter_1 11 8.77e-05 TTGCAGCAGG CAGTCAGTTTCTTCC CGTGATTTGC promoter_58 123 1.05e-04 GGAACAATGT GAGTCGCTTTTTTAG TGCAACTCAT promoter_48 35 1.05e-04 CAAGAACTCG CCGTTCGCTTCTTCC CCTGAAATGA promoter_46 1 1.14e-04 . CAGGCGTTTTCTGTT CTTTACTACT promoter_4 94 1.24e-04 CTATTTATAG CGGCCTCATTTTTCC CCCGAACATG promoter_41 118 1.35e-04 GATTTGCCGG TTGTCGGCATCTTTC TAAACGTAAG promoter_21 46 1.87e-04 CCTTCACTGC CCGTTGCCGTCAGTT ACTCCCGCTA promoter_10 12 1.87e-04 ACAACAATCG CAGTTGCAATTATTG CGTACAGCCA promoter_30 14 2.03e-04 TTCGGTCAAT CTGTCACGTTTACCT TACGAGCCCA promoter_68 107 2.55e-04 CAGCCAGCTT CCCGCGCCGTTTATG CTATCGACAA promoter_34 59 2.55e-04 CACAAGGTGA TAGATGCGTTTTCAC CCGCGGGCTG promoter_26 18 2.55e-04 GGAGACGGTT CTGGGGGCTATTTTC CCCGCCAACT promoter_51 121 2.75e-04 CACATAATTG CTGTTTGTTTTTTAA CCAAGGTATC promoter_64 3 2.96e-04 TT CACTTTGGTTTTGTC AGGCTTGCGG promoter_57 23 3.18e-04 AGAATATTAC CCGCCGTGGTTAGCG AAAGCTGGCA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CWGNYGCBTTTTTTB MEME-1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- promoter_14 1.7e-07 14_[+1]_121 promoter_72 7.9e-07 29_[+1]_106 promoter_31 1.3e-06 48_[+1]_87 promoter_36 2.4e-06 20_[+1]_115 promoter_2 3.8e-06 85_[+1]_50 promoter_40 8.4e-06 124_[+1]_11 promoter_24 8.4e-06 107_[+1]_28 promoter_3 8.4e-06 59_[+1]_76 promoter_61 9.5e-06 100_[+1]_35 promoter_74 1.1e-05 88_[+1]_47 promoter_69 1.5e-05 33_[+1]_102 promoter_60 1.5e-05 114_[+1]_21 promoter_35 1.5e-05 65_[+1]_70 promoter_53 1.9e-05 9_[+1]_126 promoter_63 2.7e-05 61_[+1]_74 promoter_37 3e-05 86_[+1]_49 promoter_25 4.1e-05 82_[+1]_53 promoter_18 5.5e-05 56_[+1]_79 promoter_15 6.1e-05 75_[+1]_60 promoter_20 6.7e-05 100_[+1]_35 promoter_17 6.7e-05 [+1]_135 promoter_49 7.3e-05 125_[+1]_10 promoter_44 7.3e-05 124_[+1]_11 promoter_1 8.8e-05 10_[+1]_125 promoter_58 0.0001 122_[+1]_13 promoter_48 0.0001 34_[+1]_101 promoter_46 0.00011 [+1]_135 promoter_4 0.00012 93_[+1]_42 promoter_41 0.00014 117_[+1]_18 promoter_21 0.00019 45_[+1]_90 promoter_10 0.00019 11_[+1]_124 promoter_30 0.0002 13_[+1]_122 promoter_68 0.00026 106_[+1]_29 promoter_34 0.00026 58_[+1]_77 promoter_26 0.00026 17_[+1]_118 promoter_51 0.00027 120_[+1]_15 promoter_64 0.0003 2_[+1]_133 promoter_57 0.00032 22_[+1]_113 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CWGNYGCBTTTTTTB MEME-1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF CWGNYGCBTTTTTTB width=15 seqs=38 promoter_14 ( 15) CTGCCGCTTTTTTTT 1 promoter_72 ( 30) CTGGCGCTTTTTGTT 1 promoter_31 ( 49) TAGCCGCCTTTTTTC 1 promoter_36 ( 21) CCGACTCCTTTTTTG 1 promoter_2 ( 86) CTGACGCTTTTTATC 1 promoter_40 ( 125) CAGCCCCCTTTATTG 1 promoter_24 ( 108) CAGGCGGCTTTTTTA 1 promoter_3 ( 60) CAGTCGTTTTTTTTT 1 promoter_61 ( 101) TTGGCGCGTTCTTTG 1 promoter_74 ( 89) CTGTCGGTGTTATCG 1 promoter_69 ( 34) CCGCGGCGTTTTTTC 1 promoter_60 ( 115) CTGGCGGTGTTATCG 1 promoter_35 ( 66) CTGATGCCGTTTCCC 1 promoter_53 ( 10) TTGATGCCTTTATCG 1 promoter_63 ( 62) CTGATTGGTTTTGTC 1 promoter_37 ( 87) TTGTTGGTTTTTGCG 1 promoter_25 ( 83) CTGGTACGTTTTGCG 1 promoter_18 ( 57) CTGATGCCGTTTCAC 1 promoter_15 ( 76) CACTCCCCTTTTGTG 1 promoter_20 ( 101) CTGCCTTTTTCTTTG 1 promoter_17 ( 1) CGGCTCCCTTTTTTT 1 promoter_49 ( 126) ATGATGCCGTTTTTC 1 promoter_44 ( 125) TTGACGCATTTATTT 1 promoter_1 ( 11) CAGTCAGTTTCTTCC 1 promoter_58 ( 123) GAGTCGCTTTTTTAG 1 promoter_48 ( 35) CCGTTCGCTTCTTCC 1 promoter_46 ( 1) CAGGCGTTTTCTGTT 1 promoter_4 ( 94) CGGCCTCATTTTTCC 1 promoter_41 ( 118) TTGTCGGCATCTTTC 1 promoter_21 ( 46) CCGTTGCCGTCAGTT 1 promoter_10 ( 12) CAGTTGCAATTATTG 1 promoter_30 ( 14) CTGTCACGTTTACCT 1 promoter_68 ( 107) CCCGCGCCGTTTATG 1 promoter_34 ( 59) TAGATGCGTTTTCAC 1 promoter_26 ( 18) CTGGGGGCTATTTTC 1 promoter_51 ( 121) CTGTTTGTTTTTTAA 1 promoter_64 ( 3) CACTTTGGTTTTGTC 1 promoter_57 ( 23) CCGCCGTGGTTAGCG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CWGNYGCBTTTTTTB MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 10064 bayes= 8.73281 E= 9.4e-001 -336 176 -311 -58 9 -52 -211 86 -1189 -152 202 -1189 -19 -10 -11 31 -1189 136 -211 42 -178 -110 153 -80 -1189 142 35 -139 -178 81 -11 19 -236 -1189 -11 142 -336 -1189 -1189 182 -1189 -29 -1189 156 -19 -1189 -1189 147 -236 -110 6 113 -136 36 -1189 113 -236 71 70 -39 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CWGNYGCBTTTTTTB MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 38 E= 9.4e-001 0.026316 0.763158 0.026316 0.184211 0.289474 0.157895 0.052632 0.500000 0.000000 0.078947 0.921053 0.000000 0.236842 0.210526 0.210526 0.342105 0.000000 0.578947 0.052632 0.368421 0.078947 0.105263 0.657895 0.157895 0.000000 0.605263 0.289474 0.105263 0.078947 0.394737 0.210526 0.315789 0.052632 0.000000 0.210526 0.736842 0.026316 0.000000 0.000000 0.973684 0.000000 0.184211 0.000000 0.815789 0.236842 0.000000 0.000000 0.763158 0.052632 0.105263 0.236842 0.605263 0.105263 0.289474 0.000000 0.605263 0.052632 0.368421 0.368421 0.210526 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CWGNYGCBTTTTTTB MEME-1 regular expression -------------------------------------------------------------------------------- C[TA]G[TACG][CT]G[CG][CTG][TG]TT[TA][TG][TC][CGT] -------------------------------------------------------------------------------- Time 6.73 secs. ******************************************************************************** ******************************************************************************** MOTIF MWWAMGCWMYAWCACGCADTRTRKGYKA MEME-2 width = 28 sites = 11 llr = 185 E-value = 1.1e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif MWWAMGCWMYAWCACGCADTRTRKGYKA MEME-2 Description -------------------------------------------------------------------------------- Simplified A 654751153275:5:::95:4151:117 pos.-specific C 4::1426:54::716:8::1:::1:5:: probability G :21:16321:3:122a21316255a:52 matrix T :452:1:325:5222:::38:7:4:541 bits 2.1 * * 1.9 * * 1.7 * * 1.5 *** * Relative 1.3 *** * Entropy 1.1 * * * *** ** * * (24.3 bits) 0.9 * * * *** **** **** * * 0.6 * ***** *** **** **** **** 0.4 ******** **** ************** 0.2 **************************** 0.0 ---------------------------- Multilevel AATAAGCACTAACACGCAATGTGGGCGA consensus CTA C GTACGT G A AT TT sequence T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif MWWAMGCWMYAWCACGCADTRTRKGYKA MEME-2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------------------- promoter_35 10 7.11e-12 GATACCGAC ATTAAGCTCAATCGCGCATTGTGGGTGA TGGCAGAAAC promoter_18 1 7.11e-12 . ATTAAGCTCAATCGCGCATTGTGGGTGA TGGCAGAAAC promoter_20 48 1.56e-11 CTGAACGAAA ATAAAGCAGTAACCCGCAATGTGTGCGA ATTATTGGCA promoter_11 56 2.97e-09 CATAACCGCA CGATCGGATCATCACGCAATGTATGCTG ATTCGCGCGG promoter_59 16 6.29e-09 AGGAATTATG CAAACGCATCAATACGCAATGTACGTTT GTCGAAAATC promoter_62 93 1.75e-08 TCCGCTAATA AATAACAACTAACAGGGAGTAAAGGCGA TGGGAATTAA promoter_16 5 4.06e-08 TATT AAGACGCGCTAACACGGAACAGGTGCAA AATCGGCGTA promoter_43 72 4.69e-08 TAACGGTTAA CTTAACGGATGTTTCGCGGTGTGGGTGA GCATGATGGT promoter_33 116 5.03e-08 AAACCCAATA CGTAATCAACGACTTGCAATATAGGATA ACGAATC promoter_65 54 1.70e-07 TCGATCCATT AATTCGCACCGAGATGCAGGATGAGCTG GTAAAATTAC promoter_38 34 1.91e-07 TTGGCAAGAC AAACGAGTATATCAGGCATTGGATGTGA ATAAAGCGTA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif MWWAMGCWMYAWCACGCADTRTRKGYKA MEME-2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- promoter_35 7.1e-12 9_[+2]_113 promoter_18 7.1e-12 [+2]_122 promoter_20 1.6e-11 47_[+2]_75 promoter_11 3e-09 55_[+2]_67 promoter_59 6.3e-09 15_[+2]_107 promoter_62 1.8e-08 92_[+2]_30 promoter_16 4.1e-08 4_[+2]_118 promoter_43 4.7e-08 71_[+2]_51 promoter_33 5e-08 115_[+2]_7 promoter_65 1.7e-07 53_[+2]_69 promoter_38 1.9e-07 33_[+2]_89 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif MWWAMGCWMYAWCACGCADTRTRKGYKA MEME-2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF MWWAMGCWMYAWCACGCADTRTRKGYKA width=28 seqs=11 promoter_35 ( 10) ATTAAGCTCAATCGCGCATTGTGGGTGA 1 promoter_18 ( 1) ATTAAGCTCAATCGCGCATTGTGGGTGA 1 promoter_20 ( 48) ATAAAGCAGTAACCCGCAATGTGTGCGA 1 promoter_11 ( 56) CGATCGGATCATCACGCAATGTATGCTG 1 promoter_59 ( 16) CAAACGCATCAATACGCAATGTACGTTT 1 promoter_62 ( 93) AATAACAACTAACAGGGAGTAAAGGCGA 1 promoter_16 ( 5) AAGACGCGCTAACACGGAACAGGTGCAA 1 promoter_43 ( 72) CTTAACGGATGTTTCGCGGTGTGGGTGA 1 promoter_33 ( 116) CGTAATCAACGACTTGCAATATAGGATA 1 promoter_65 ( 54) AATTCGCACCGAGATGCAGGATGAGCTG 1 promoter_38 ( 34) AAACGAGTATATCAGGCATTGGATGTGA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif MWWAMGCWMYAWCACGCADTRTRKGYKA MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 28 n= 9102 bayes= 9.79985 E= 1.1e+001 123 69 -1010 -1010 75 -1010 -32 40 42 -1010 -132 98 142 -131 -1010 -60 101 69 -132 -1010 -157 -31 148 -160 -157 149 26 -1010 101 -1010 -32 -2 1 101 -132 -60 -58 69 -1010 72 142 -1010 26 -1010 101 -1010 -1010 72 -1010 169 -132 -60 101 -131 -32 -60 -1010 149 -32 -60 -1010 -1010 214 -1010 -1010 186 -32 -1010 174 -1010 -132 -1010 75 -1010 26 -2 -1010 -131 -132 157 42 -1010 148 -1010 -157 -1010 -32 140 75 -1010 126 -1010 -157 -131 100 40 -1010 -1010 214 -1010 -157 101 -1010 72 -157 -1010 126 40 142 -1010 -32 -160 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif MWWAMGCWMYAWCACGCADTRTRKGYKA MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 28 nsites= 11 E= 1.1e+001 0.636364 0.363636 0.000000 0.000000 0.454545 0.000000 0.181818 0.363636 0.363636 0.000000 0.090909 0.545455 0.727273 0.090909 0.000000 0.181818 0.545455 0.363636 0.090909 0.000000 0.090909 0.181818 0.636364 0.090909 0.090909 0.636364 0.272727 0.000000 0.545455 0.000000 0.181818 0.272727 0.272727 0.454545 0.090909 0.181818 0.181818 0.363636 0.000000 0.454545 0.727273 0.000000 0.272727 0.000000 0.545455 0.000000 0.000000 0.454545 0.000000 0.727273 0.090909 0.181818 0.545455 0.090909 0.181818 0.181818 0.000000 0.636364 0.181818 0.181818 0.000000 0.000000 1.000000 0.000000 0.000000 0.818182 0.181818 0.000000 0.909091 0.000000 0.090909 0.000000 0.454545 0.000000 0.272727 0.272727 0.000000 0.090909 0.090909 0.818182 0.363636 0.000000 0.636364 0.000000 0.090909 0.000000 0.181818 0.727273 0.454545 0.000000 0.545455 0.000000 0.090909 0.090909 0.454545 0.363636 0.000000 0.000000 1.000000 0.000000 0.090909 0.454545 0.000000 0.454545 0.090909 0.000000 0.545455 0.363636 0.727273 0.000000 0.181818 0.090909 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif MWWAMGCWMYAWCACGCADTRTRKGYKA MEME-2 regular expression -------------------------------------------------------------------------------- [AC][AT][TA]A[AC]G[CG][AT][CA][TC][AG][AT]CACGCA[AGT]T[GA]T[GA][GT]G[CT][GT]A -------------------------------------------------------------------------------- Time 12.78 secs. ******************************************************************************** ******************************************************************************** MOTIF RTDACAVMGRAAAHA MEME-3 width = 15 sites = 23 llr = 216 E-value = 1.2e+003 ******************************************************************************** -------------------------------------------------------------------------------- Motif RTDACAVMGRAAAHA MEME-3 Description -------------------------------------------------------------------------------- Simplified A 4:26:a43:479949 pos.-specific C :1:1a:352121131 probability G 4:42::3:831:::: matrix T 2931:::2:2:::3: bits 2.1 1.9 * 1.7 ** 1.5 * ** ** Relative 1.3 * ** * ** * Entropy 1.1 * ** * ** * (13.5 bits) 0.9 * ** * ** * 0.6 * ** * *** * 0.4 *** ***** *** * 0.2 *************** 0.0 --------------- Multilevel ATGACAACGAAAAAA consensus G T CA GC C sequence A G T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RTDACAVMGRAAAHA MEME-3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------- promoter_48 90 9.56e-08 GCCTTATGTG ATTACAACGAAAATA AAAACCATCA promoter_40 90 1.58e-06 TATTCGTCAC GTGACAGTGACAAAA AGGCTCTATA promoter_37 58 2.36e-06 AAAAGCTTCC TTGTCAGCGAAAAAA ATTAAAGCGC promoter_41 13 2.67e-06 GTTGCGCAAT TTGTCAACGAAAACA ATAATGCGTA promoter_42 126 3.39e-06 GAATAAGGTT TTTACAACCAAAAAA GAAGGTCGTT promoter_12 124 6.04e-06 TCAATGAAAA ATTGCACAGTAAACA TGGGGTTATG promoter_47 75 8.29e-06 TCCTCGTAAA ATTGCAACGCCAACA CCATCTTCCT promoter_63 2 1.01e-05 C GTAACACCGTACAAA ATGATTTTGA promoter_61 23 1.01e-05 TTGCTTGACA GCTTCACCGAAAAAA TGGCGCGAAA promoter_45 15 1.49e-05 CGTCTACAGC ATGACAAACAAAAAC AGATGCGTTA promoter_56 111 1.96e-05 GCTGGCGTTG ATGCCAGCGGCAAAC CGAATTAATC promoter_49 38 2.14e-05 CTGGGTATAC GTAACAATGGACAAA TGTGGTACAT promoter_9 77 2.34e-05 ATTGATTTCC GTGGCGCAGAAAAAA GCAAATGGCA promoter_51 91 2.77e-05 TGTGGAAAAA GTTACACTGCGAATA TTCGGCACAT promoter_64 128 3.01e-05 GTTTCAGAAA ATAACAGCTGAAATA ATCTCGCG promoter_32 26 3.01e-05 TGATGCAATA GTGAAAACGGCAATA CGCCACGCGC promoter_17 134 3.54e-05 TTTCCGACTA TTAACAGAGAGAATA TT promoter_10 122 3.54e-05 CGCGCCGTGA GTACCACCGTAACAA GCAGGCATAC promoter_65 87 3.84e-05 AGCTGGTAAA ATTACAGGCGAAACA TCAGCGCACC promoter_1 45 3.84e-05 CGCCATGACC ATGACAATGAAAAGC CACTTCTTTC promoter_20 126 4.15e-05 ACTCTATGAC GTTACAAAGTTAATA TGCGCGCCCT promoter_71 110 5.62e-05 CTGCTGGATA ATGCCACCGCCACCA TCAACCCCGG promoter_44 21 7.47e-05 CCAGGTTGCC ACGGCACACGAAACA GCGTTGGTCC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RTDACAVMGRAAAHA MEME-3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- promoter_48 9.6e-08 89_[+3]_46 promoter_40 1.6e-06 89_[+3]_46 promoter_37 2.4e-06 57_[+3]_78 promoter_41 2.7e-06 12_[+3]_123 promoter_42 3.4e-06 125_[+3]_10 promoter_12 6e-06 123_[+3]_12 promoter_47 8.3e-06 74_[+3]_61 promoter_63 1e-05 1_[+3]_134 promoter_61 1e-05 22_[+3]_113 promoter_45 1.5e-05 14_[+3]_121 promoter_56 2e-05 110_[+3]_25 promoter_49 2.1e-05 37_[+3]_98 promoter_9 2.3e-05 76_[+3]_59 promoter_51 2.8e-05 90_[+3]_45 promoter_64 3e-05 127_[+3]_8 promoter_32 3e-05 25_[+3]_110 promoter_17 3.5e-05 133_[+3]_2 promoter_10 3.5e-05 121_[+3]_14 promoter_65 3.8e-05 86_[+3]_49 promoter_1 3.8e-05 44_[+3]_91 promoter_20 4.2e-05 125_[+3]_10 promoter_71 5.6e-05 109_[+3]_26 promoter_44 7.5e-05 20_[+3]_115 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RTDACAVMGRAAAHA MEME-3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF RTDACAVMGRAAAHA width=15 seqs=23 promoter_48 ( 90) ATTACAACGAAAATA 1 promoter_40 ( 90) GTGACAGTGACAAAA 1 promoter_37 ( 58) TTGTCAGCGAAAAAA 1 promoter_41 ( 13) TTGTCAACGAAAACA 1 promoter_42 ( 126) TTTACAACCAAAAAA 1 promoter_12 ( 124) ATTGCACAGTAAACA 1 promoter_47 ( 75) ATTGCAACGCCAACA 1 promoter_63 ( 2) GTAACACCGTACAAA 1 promoter_61 ( 23) GCTTCACCGAAAAAA 1 promoter_45 ( 15) ATGACAAACAAAAAC 1 promoter_56 ( 111) ATGCCAGCGGCAAAC 1 promoter_49 ( 38) GTAACAATGGACAAA 1 promoter_9 ( 77) GTGGCGCAGAAAAAA 1 promoter_51 ( 91) GTTACACTGCGAATA 1 promoter_64 ( 128) ATAACAGCTGAAATA 1 promoter_32 ( 26) GTGAAAACGGCAATA 1 promoter_17 ( 134) TTAACAGAGAGAATA 1 promoter_10 ( 122) GTACCACCGTAACAA 1 promoter_65 ( 87) ATTACAGGCGAAACA 1 promoter_1 ( 45) ATGACAATGAAAAGC 1 promoter_20 ( 126) GTTACAAAGTTAATA 1 promoter_71 ( 110) ATGCCACCGCCACCA 1 promoter_44 ( 21) ACGGCACACGAAACA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RTDACAVMGRAAAHA MEME-3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 10064 bayes= 8.92939 E= 1.2e+003 68 -1117 78 -67 -1117 -138 -1117 173 -32 -1117 94 33 106 -79 -39 -108 -264 208 -1117 -1117 182 -1117 -238 -1117 53 62 20 -1117 -6 121 -238 -67 -1117 -38 178 -266 68 -79 20 -67 127 -5 -139 -266 175 -138 -1117 -1117 175 -138 -1117 -1117 68 21 -238 -8 168 -79 -1117 -1117 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RTDACAVMGRAAAHA MEME-3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 23 E= 1.2e+003 0.434783 0.000000 0.391304 0.173913 0.000000 0.086957 0.000000 0.913043 0.217391 0.000000 0.434783 0.347826 0.565217 0.130435 0.173913 0.130435 0.043478 0.956522 0.000000 0.000000 0.956522 0.000000 0.043478 0.000000 0.391304 0.347826 0.260870 0.000000 0.260870 0.521739 0.043478 0.173913 0.000000 0.173913 0.782609 0.043478 0.434783 0.130435 0.260870 0.173913 0.652174 0.217391 0.086957 0.043478 0.913043 0.086957 0.000000 0.000000 0.913043 0.086957 0.000000 0.000000 0.434783 0.260870 0.043478 0.260870 0.869565 0.130435 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RTDACAVMGRAAAHA MEME-3 regular expression -------------------------------------------------------------------------------- [AG]T[GTA]ACA[ACG][CA]G[AG][AC]AA[ACT]A -------------------------------------------------------------------------------- Time 18.73 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- promoter_1 2.71e-03 10_[+1(8.77e-05)]_19_[+3(3.84e-05)]_\ 91 promoter_2 1.01e-04 85_[+1(3.78e-06)]_20_[+2(6.91e-05)]_\ 2 promoter_3 9.85e-03 59_[+1(8.40e-06)]_76 promoter_4 1.58e-01 150 promoter_5 3.31e-01 150 promoter_6 7.74e-01 150 promoter_7 4.42e-01 150 promoter_8 9.91e-01 150 promoter_9 5.68e-02 76_[+3(2.34e-05)]_59 promoter_10 3.84e-03 121_[+3(3.54e-05)]_14 promoter_11 7.57e-06 55_[+2(2.97e-09)]_67 promoter_12 2.32e-02 123_[+3(6.04e-06)]_12 promoter_13 9.35e-01 150 promoter_14 4.39e-04 14_[+1(1.73e-07)]_121 promoter_15 4.49e-02 75_[+1(6.05e-05)]_60 promoter_16 4.66e-05 4_[+2(4.06e-08)]_118 promoter_17 3.93e-04 [+1(6.66e-05)]_118_[+3(3.54e-05)]_2 promoter_18 2.22e-09 [+2(7.11e-12)]_28_[+1(5.50e-05)]_79 promoter_19 5.42e-01 150 promoter_20 4.68e-11 47_[+2(1.56e-11)]_25_[+1(6.66e-05)]_\ 10_[+3(4.15e-05)]_10 promoter_21 2.31e-01 150 promoter_22 4.44e-01 150 promoter_23 6.69e-01 150 promoter_24 9.15e-04 107_[+1(8.40e-06)]_28 promoter_25 3.53e-02 82_[+1(4.09e-05)]_53 promoter_26 1.96e-02 150 promoter_27 5.88e-01 150 promoter_28 2.26e-01 150 promoter_29 4.34e-01 150 promoter_30 4.71e-02 150 promoter_31 8.12e-04 48_[+1(1.31e-06)]_87 promoter_32 1.87e-02 25_[+3(3.01e-05)]_110 promoter_33 3.35e-05 115_[+2(5.03e-08)]_7 promoter_34 2.60e-01 150 promoter_35 6.90e-10 9_[+2(7.11e-12)]_28_[+1(1.54e-05)]_\ 70 promoter_36 9.75e-03 20_[+1(2.44e-06)]_115 promoter_37 6.84e-05 57_[+3(2.36e-06)]_14_[+1(2.99e-05)]_\ 49 promoter_38 4.37e-04 33_[+2(1.91e-07)]_89 promoter_39 2.16e-01 150 promoter_40 1.02e-05 89_[+3(1.58e-06)]_20_[+1(8.40e-06)]_\ 11 promoter_41 3.46e-04 12_[+3(2.67e-06)]_123 promoter_42 2.68e-03 125_[+3(3.39e-06)]_10 promoter_43 2.66e-04 71_[+2(4.69e-08)]_51 promoter_44 2.79e-03 20_[+3(7.47e-05)]_89_[+1(7.31e-05)]_\ 11 promoter_45 2.74e-02 14_[+3(1.49e-05)]_121 promoter_46 9.52e-02 150 promoter_47 1.00e-02 74_[+3(8.29e-06)]_61 promoter_48 1.43e-05 89_[+3(9.56e-08)]_46 promoter_49 5.66e-04 37_[+3(2.14e-05)]_73_[+1(7.31e-05)]_\ 10 promoter_50 3.43e-01 150 promoter_51 1.71e-03 90_[+3(2.77e-05)]_45 promoter_52 1.01e-01 150 promoter_53 2.06e-02 9_[+1(1.93e-05)]_126 promoter_54 7.76e-01 150 promoter_55 4.35e-01 150 promoter_56 3.03e-02 110_[+3(1.96e-05)]_25 promoter_57 2.59e-01 150 promoter_58 2.06e-02 150 promoter_59 5.01e-05 15_[+2(6.29e-09)]_107 promoter_60 5.12e-02 78_[+1(6.66e-05)]_21_[+1(1.54e-05)]_\ 21 promoter_61 9.27e-05 22_[+3(1.01e-05)]_63_[+1(9.52e-06)]_\ 35 promoter_62 7.19e-05 92_[+2(1.75e-08)]_30 promoter_63 3.86e-04 1_[+3(1.01e-05)]_45_[+1(2.69e-05)]_\ 74 promoter_64 4.36e-03 127_[+3(3.01e-05)]_8 promoter_65 4.21e-06 53_[+2(1.70e-07)]_5_[+3(3.84e-05)]_\ 49 promoter_66 5.77e-01 150 promoter_67 3.67e-02 150 promoter_68 2.31e-01 150 promoter_69 3.14e-02 33_[+1(1.54e-05)]_102 promoter_70 7.49e-01 150 promoter_71 8.20e-03 109_[+3(5.62e-05)]_26 promoter_72 2.61e-03 29_[+1(7.89e-07)]_106 promoter_73 5.93e-01 150 promoter_74 1.19e-02 88_[+1(1.08e-05)]_47 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (3) found. ******************************************************************************** CPU: noble-meme.grid.gs.washington.edu ********************************************************************************