******************************************************************************** MEME - Motif discovery tool ******************************************************************************** MEME version 5.3.3 (Release date: Sun Feb 7 15:39:52 2021 -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= ../result/final_prediction/worm/fasta/RankLinear2.0_40/daf-12.fasta CONTROL SEQUENCES= --none-- ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ chrV:14368801-14368881 1.0000 80 chrIII:12841531-12841611 1.0000 80 chrV:12529078-12529158 1.0000 80 chrX:11478905-11478985 1.0000 80 chrII:8130947-8131027 1.0000 80 chrV:14366704-14366784 1.0000 80 chrX:11482321-11482401 1.0000 80 chrV:12537672-12537752 1.0000 80 chrI:14620901-14620981 1.0000 80 chrII:11619287-11619367 1.0000 80 chrII:1238085-1238165 1.0000 80 chrIV:8793501-8793581 1.0000 80 chrV:12540106-12540186 1.0000 80 chrX:535881-535961 1.0000 80 chrX:7230546-7230626 1.0000 80 chrIV:11063222-11063302 1.0000 80 chrV:11733596-11733676 1.0000 80 chrX:14334310-14334390 1.0000 80 chrIII:9766319-9766399 1.0000 80 chrI:1691195-1691275 1.0000 80 chrX:14561703-14561783 1.0000 80 chrIV:5607487-5607567 1.0000 80 chrV:12528355-12528435 1.0000 80 chrX:5653913-5653993 1.0000 80 chrV:12530271-12530351 1.0000 80 chrIII:12849378-12849458 1.0000 80 chrI:999215-999295 1.0000 80 chrV:12533905-12533985 1.0000 80 chrX:10640613-10640693 1.0000 80 chrII:11620126-11620206 1.0000 80 chrIV:14033149-14033229 1.0000 80 chrIII:4195284-4195364 1.0000 80 chrV:5523307-5523387 1.0000 80 chrX:10637620-10637700 1.0000 80 chrX:16024800-16024880 1.0000 80 chrII:9617859-9617939 1.0000 80 chrIV:1070530-1070610 1.0000 80 chrIII:4568733-4568813 1.0000 80 chrV:14347329-14347409 1.0000 80 chrV:265214-265294 1.0000 80 chrIV:8529107-8529187 1.0000 80 chrV:5271594-5271674 1.0000 80 chrV:11147998-11148078 1.0000 80 chrIV:9511286-9511366 1.0000 80 chrX:12363095-12363175 1.0000 80 chrI:8786935-8787015 1.0000 80 chrIV:15472549-15472629 1.0000 80 chrIII:10407471-10407551 1.0000 80 chrX:11465368-11465448 1.0000 80 chrX:2364899-2364979 1.0000 80 chrX:16056567-16056647 1.0000 80 chrX:17505891-17505971 1.0000 80 chrI:9343953-9344033 1.0000 80 chrI:9422263-9422343 1.0000 80 chrIV:14033361-14033441 1.0000 80 chrX:2599035-2599115 1.0000 80 chrI:397908-397988 1.0000 80 chrII:2974025-2974105 1.0000 80 chrI:6835315-6835395 1.0000 80 chrX:1344968-1345048 1.0000 80 chrX:827689-827769 1.0000 80 chrII:6951524-6951604 1.0000 80 chrV:15766381-15766461 1.0000 80 chrIII:5679104-5679184 1.0000 80 chrII:12944658-12944738 1.0000 80 chrIII:12612640-12612720 1.0000 80 chrX:9958678-9958758 1.0000 80 chrIII:1925267-1925347 1.0000 80 chrIV:4445892-4445972 1.0000 80 chrX:5841221-5841301 1.0000 80 chrIII:8795851-8795931 1.0000 80 chrIV:8795161-8795241 1.0000 80 chrIII:4899852-4899932 1.0000 80 chrII:3077095-3077175 1.0000 80 chrIV:8527820-8527900 1.0000 80 ******************************************************************************** ******************************************************************************** COMMAND LINE SUMMARY ******************************************************************************** This information can also be useful in the event you wish to report a problem with the MEME software. command: meme -oc ../result/final_prediction/worm/inference_raw/MEME/RankLinear2.0_40_daf-12/ -dna -nmotifs 5 -w 8 -maxsize 250000 -nostatus ../result/final_prediction/worm/fasta/RankLinear2.0_40/daf-12.fasta model: mod= zoops nmotifs= 5 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= 8 nsites: minsites= 2 maxsites= 75 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= 6000 N= 75 sample: seed= 0 hsfrac= 0 searchsize= 6000 norand= no csites= 1000 Letter frequencies in dataset: A 0.273 C 0.225 G 0.23 T 0.273 Background letter frequencies (from file dataset with add-one prior applied): A 0.273 C 0.225 G 0.23 T 0.273 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF AAAGTRCA MEME-1 width = 8 sites = 18 llr = 164 E-value = 1.2e-006 ******************************************************************************** -------------------------------------------------------------------------------- Motif AAAGTRCA MEME-1 Description -------------------------------------------------------------------------------- Simplified A 89a:16:a pos.-specific C 21::::a: probability G :::a:4:: matrix T :1::9::: bits 2.2 * * 1.9 ** ** 1.7 ** ** 1.5 *** ** Relative 1.3 ***** ** Entropy 1.1 ******** (13.1 bits) 0.9 ******** 0.6 ******** 0.4 ******** 0.2 ******** 0.0 -------- Multilevel AAAGTACA consensus G sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAAGTRCA MEME-1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chrI:6835315-6835395 72 2.14e-05 CTAACATAGA AAAGTACA C chrX:16024800-16024880 70 2.14e-05 GGTAACATGA AAAGTACA TTT chrIII:12849378-12849458 46 2.14e-05 TTCTTTCGGA AAAGTACA CTTGTCGCCT chrV:11733596-11733676 73 2.14e-05 TTGAACTCGA AAAGTACA chrV:14366704-14366784 39 2.14e-05 CACTTTTATA AAAGTACA CGGCACCGAG chrV:14368801-14368881 65 2.14e-05 TGTACTTCTG AAAGTACA TGCGATGA chrI:999215-999295 46 3.95e-05 CCGCAAGGAA AAAGTGCA AAGAAATTAG chrX:14561703-14561783 8 3.95e-05 CAGAATA AAAGTGCA AGTGGTCGGC chrIV:8793501-8793581 49 3.95e-05 TGCACTTTGA AAAGTGCA AGTGTTGACT chrII:11619287-11619367 72 3.95e-05 TGGGGCGTTG AAAGTGCA A chrX:11482321-11482401 57 3.95e-05 GGCTGCTGAA AAAGTGCA AACTAAGGAC chrIII:12841531-12841611 63 3.95e-05 TTCGGAAGGA AAAGTGCA ACTGGTCACT chrV:5523307-5523387 18 5.71e-05 AAGTCAAGTT CAAGTACA TTTGTCCACT chrII:11620126-11620206 64 5.71e-05 CAGGCGCCTT CAAGTACA CAAACCACA chrX:5653913-5653993 23 7.20e-05 CTGTCGTTCA CAAGTGCA CTGCTGATAT chrV:12528355-12528435 24 8.97e-05 GAGGCATGCG ACAGTACA CATGCACTTT chrX:535881-535961 44 1.33e-04 AATGTGTGAG AAAGAACA TGAGACGCAG chrX:11478905-11478985 32 1.33e-04 ATCTTATGGC ATAGTACA GATGCACTTT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAAGTRCA MEME-1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrI:6835315-6835395 2.1e-05 71_[+1]_1 chrX:16024800-16024880 2.1e-05 69_[+1]_3 chrIII:12849378-12849458 2.1e-05 45_[+1]_27 chrV:11733596-11733676 2.1e-05 72_[+1] chrV:14366704-14366784 2.1e-05 38_[+1]_34 chrV:14368801-14368881 2.1e-05 64_[+1]_8 chrI:999215-999295 3.9e-05 45_[+1]_27 chrX:14561703-14561783 3.9e-05 7_[+1]_65 chrIV:8793501-8793581 3.9e-05 48_[+1]_24 chrII:11619287-11619367 3.9e-05 71_[+1]_1 chrX:11482321-11482401 3.9e-05 56_[+1]_16 chrIII:12841531-12841611 3.9e-05 62_[+1]_10 chrV:5523307-5523387 5.7e-05 17_[+1]_55 chrII:11620126-11620206 5.7e-05 63_[+1]_9 chrX:5653913-5653993 7.2e-05 22_[+1]_50 chrV:12528355-12528435 9e-05 23_[+1]_49 chrX:535881-535961 0.00013 43_[+1]_29 chrX:11478905-11478985 0.00013 31_[+1]_41 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAAGTRCA MEME-1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF AAAGTRCA width=8 seqs=18 chrI:6835315-6835395 ( 72) AAAGTACA 1 chrX:16024800-16024880 ( 70) AAAGTACA 1 chrIII:12849378-12849458 ( 46) AAAGTACA 1 chrV:11733596-11733676 ( 73) AAAGTACA 1 chrV:14366704-14366784 ( 39) AAAGTACA 1 chrV:14368801-14368881 ( 65) AAAGTACA 1 chrI:999215-999295 ( 46) AAAGTGCA 1 chrX:14561703-14561783 ( 8) AAAGTGCA 1 chrIV:8793501-8793581 ( 49) AAAGTGCA 1 chrII:11619287-11619367 ( 72) AAAGTGCA 1 chrX:11482321-11482401 ( 57) AAAGTGCA 1 chrIII:12841531-12841611 ( 63) AAAGTGCA 1 chrV:5523307-5523387 ( 18) CAAGTACA 1 chrII:11620126-11620206 ( 64) CAAGTACA 1 chrX:5653913-5653993 ( 23) CAAGTGCA 1 chrV:12528355-12528435 ( 24) ACAGTACA 1 chrX:535881-535961 ( 44) AAAGAACA 1 chrX:11478905-11478985 ( 32) ATAGTACA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAAGTRCA MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 5475 bayes= 8.37869 E= 1.2e-006 161 -43 -1081 -1081 170 -202 -1081 -229 187 -1081 -1081 -1081 -1081 -1081 212 -1081 -229 -1081 -1081 179 116 -1081 76 -1081 -1081 215 -1081 -1081 187 -1081 -1081 -1081 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAAGTRCA MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 18 E= 1.2e-006 0.833333 0.166667 0.000000 0.000000 0.888889 0.055556 0.000000 0.055556 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.055556 0.000000 0.000000 0.944444 0.611111 0.000000 0.388889 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAAGTRCA MEME-1 regular expression -------------------------------------------------------------------------------- AAAGT[AG]CA -------------------------------------------------------------------------------- Time 0.88 secs. ******************************************************************************** ******************************************************************************** MOTIF GTDAGAGA MEME-2 width = 8 sites = 25 llr = 190 E-value = 3.4e+000 ******************************************************************************** -------------------------------------------------------------------------------- Motif GTDAGAGA MEME-2 Description -------------------------------------------------------------------------------- Simplified A 3:38:a:a pos.-specific C 1::1:::: probability G 624:a:a: matrix T :821:::: bits 2.2 * * 1.9 **** 1.7 **** 1.5 **** Relative 1.3 **** Entropy 1.1 **** (11.0 bits) 0.9 ** ***** 0.6 ** ***** 0.4 ******** 0.2 ******** 0.0 -------- Multilevel GTGAGAGA consensus A A sequence T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GTDAGAGA MEME-2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chrII:2974025-2974105 54 1.55e-05 GCGTGGAAGA GTGAGAGA GCGCGAGAGA chrIV:1070530-1070610 67 1.55e-05 GAAGAGACTG GTGAGAGA ACGGGA chrIII:12849378-12849458 4 1.55e-05 TGC GTGAGAGA ATTGATGAGA chrIII:12841531-12841611 9 1.55e-05 GAAAAAGA GTGAGAGA GTATTAGAGA chrII:11620126-11620206 19 3.40e-05 GACACAGACA GTAAGAGA GATAGAAATG chrIV:8795161-8795241 4 5.24e-05 GGA GTTAGAGA AAAGAAAGGA chrIII:8795851-8795931 43 5.24e-05 CTGAAGAGGT GTTAGAGA AATAGAGAAA chrI:9343953-9344033 6 5.24e-05 AGATG GTTAGAGA AAGAGTGAAA chrII:9617859-9617939 21 8.40e-05 gaaatcgaag gggagaga gagaaaaggg chrII:1238085-1238165 21 8.40e-05 CACTTGGGAC GGGAGAGA GAGAGGGGGG chrIII:10407471-10407551 2 1.06e-04 C ATAAGAGA TGGCGTTCTC chrI:1691195-1691275 57 1.06e-04 TCTCTTAGTC ATAAGAGA TAGTACTATA chrII:3077095-3077175 66 1.19e-04 CCACGTCACT GTGCGAGA AATCTAG chrI:999215-999295 59 1.41e-04 GTGCAAAGAA ATTAGAGA AAAAAGACCG chrV:12528355-12528435 60 1.72e-04 TTTCAATTGA GGAAGAGA CTATTTGAAA chrII:11619287-11619367 28 1.87e-04 CAACAACAAA CTGAGAGA CCGAGACGAA chrIV:8527820-8527900 59 2.18e-04 GTGAGAGTTT GGTAGAGA AGTGATAGTC chrIV:15472549-15472629 30 2.18e-04 GCCGTAGAGA GTACGAGA CGCAGAAATC chrX:7230546-7230626 13 2.36e-04 GTTGTTGTCA GTATGAGA CCAAGGCCAG chrX:17505891-17505971 37 2.85e-04 TGTGCCCGTG CTAAGAGA CCAAACACCA chrX:11482321-11482401 31 3.31e-04 CGATTAGAAT ATGCGAGA CTCAGCGTGG chrI:8786935-8787015 25 4.02e-04 ATGAGATAGT ATGTGAGA CATAGAGACG chrIV:9511286-9511366 48 4.02e-04 TTGGAATAGG ATGTGAGA TTATATTTAA chrX:535881-535961 65 5.64e-04 GACGCAGATA GCTAGAGA GGTGAAAA chrI:9422263-9422343 19 8.65e-04 CTTTAAATGG AAAAGAGA TCCAACCGAA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GTDAGAGA MEME-2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrII:2974025-2974105 1.6e-05 53_[+2]_19 chrIV:1070530-1070610 1.6e-05 66_[+2]_6 chrIII:12849378-12849458 1.6e-05 3_[+2]_69 chrIII:12841531-12841611 1.6e-05 8_[+2]_64 chrII:11620126-11620206 3.4e-05 18_[+2]_54 chrIV:8795161-8795241 5.2e-05 3_[+2]_69 chrIII:8795851-8795931 5.2e-05 42_[+2]_30 chrI:9343953-9344033 5.2e-05 5_[+2]_67 chrII:9617859-9617939 8.4e-05 20_[+2]_52 chrII:1238085-1238165 8.4e-05 20_[+2]_52 chrIII:10407471-10407551 0.00011 1_[+2]_71 chrI:1691195-1691275 0.00011 56_[+2]_16 chrII:3077095-3077175 0.00012 65_[+2]_7 chrI:999215-999295 0.00014 58_[+2]_14 chrV:12528355-12528435 0.00017 59_[+2]_13 chrII:11619287-11619367 0.00019 27_[+2]_45 chrIV:8527820-8527900 0.00022 58_[+2]_14 chrIV:15472549-15472629 0.00022 29_[+2]_43 chrX:7230546-7230626 0.00024 12_[+2]_60 chrX:17505891-17505971 0.00028 36_[+2]_36 chrX:11482321-11482401 0.00033 30_[+2]_42 chrI:8786935-8787015 0.0004 24_[+2]_48 chrIV:9511286-9511366 0.0004 47_[+2]_25 chrX:535881-535961 0.00056 64_[+2]_8 chrI:9422263-9422343 0.00086 18_[+2]_54 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GTDAGAGA MEME-2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF GTDAGAGA width=8 seqs=25 chrII:2974025-2974105 ( 54) GTGAGAGA 1 chrIV:1070530-1070610 ( 67) GTGAGAGA 1 chrIII:12849378-12849458 ( 4) GTGAGAGA 1 chrIII:12841531-12841611 ( 9) GTGAGAGA 1 chrII:11620126-11620206 ( 19) GTAAGAGA 1 chrIV:8795161-8795241 ( 4) GTTAGAGA 1 chrIII:8795851-8795931 ( 43) GTTAGAGA 1 chrI:9343953-9344033 ( 6) GTTAGAGA 1 chrII:9617859-9617939 ( 21) GGGAGAGA 1 chrII:1238085-1238165 ( 21) GGGAGAGA 1 chrIII:10407471-10407551 ( 2) ATAAGAGA 1 chrI:1691195-1691275 ( 57) ATAAGAGA 1 chrII:3077095-3077175 ( 66) GTGCGAGA 1 chrI:999215-999295 ( 59) ATTAGAGA 1 chrV:12528355-12528435 ( 60) GGAAGAGA 1 chrII:11619287-11619367 ( 28) CTGAGAGA 1 chrIV:8527820-8527900 ( 59) GGTAGAGA 1 chrIV:15472549-15472629 ( 30) GTACGAGA 1 chrX:7230546-7230626 ( 13) GTATGAGA 1 chrX:17505891-17505971 ( 37) CTAAGAGA 1 chrX:11482321-11482401 ( 31) ATGCGAGA 1 chrI:8786935-8787015 ( 25) ATGTGAGA 1 chrIV:9511286-9511366 ( 48) ATGTGAGA 1 chrX:535881-535961 ( 65) GCTAGAGA 1 chrI:9422263-9422343 ( 19) AAAAGAGA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GTDAGAGA MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 5475 bayes= 8.26014 E= 3.4e+000 4 -149 148 -1129 -277 -249 -52 148 23 -1129 94 -18 148 -91 -1129 -118 -1129 -1129 212 -1129 187 -1129 -1129 -1129 -1129 -1129 212 -1129 187 -1129 -1129 -1129 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GTDAGAGA MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 25 E= 3.4e+000 0.280000 0.080000 0.640000 0.000000 0.040000 0.040000 0.160000 0.760000 0.320000 0.000000 0.440000 0.240000 0.760000 0.120000 0.000000 0.120000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GTDAGAGA MEME-2 regular expression -------------------------------------------------------------------------------- [GA]T[GAT]AGAGA -------------------------------------------------------------------------------- Time 1.65 secs. ******************************************************************************** ******************************************************************************** MOTIF ACACACWC MEME-3 width = 8 sites = 12 llr = 105 E-value = 1.3e+003 ******************************************************************************** -------------------------------------------------------------------------------- Motif ACACACWC MEME-3 Description -------------------------------------------------------------------------------- Simplified A a1a:9:61 pos.-specific C :8:a:9:8 probability G :::::1:1 matrix T :1::1:4: bits 2.2 * 1.9 * ** 1.7 * ** * 1.5 * **** Relative 1.3 ****** * Entropy 1.1 ****** * (12.6 bits) 0.9 ******** 0.6 ******** 0.4 ******** 0.2 ******** 0.0 -------- Multilevel ACACACAC consensus T sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ACACACWC MEME-3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chrIII:4899852-4899932 36 1.42e-05 CACACGCATG ACACACAC TTTCGCGGCC chrIII:1925267-1925347 73 1.42e-05 ACCGGGCTTc acacacac chrIV:5607487-5607567 11 1.42e-05 AGGGGTACAC ACACACAC ACATTCATAG chrV:12537672-12537752 21 1.42e-05 TTTCTGGCGC ACACACAC TCACCATTCT chrIII:10407471-10407551 55 2.85e-05 TCTCACGGCC ACACACTC TCTCGTCGCG chrX:11478905-11478985 72 2.85e-05 CCGTTCGCAT ACACACTC G chrII:11620126-11620206 10 7.18e-05 TCACTAGAG ACACAGAC AGTAAGAGAG chrX:2599035-2599115 1 1.24e-04 . ACACACAA AGTAGCTGGT chrX:10640613-10640693 41 1.24e-04 GGCTTTTGTA AAACACAC CTTCGCTTAT chrX:17505891-17505971 21 1.38e-04 TCCTCACTCT ACACACTG TGCCCGTGCT chrX:9958678-9958758 5 1.67e-04 TCTT ACACTCTC CAAgtctgtg chrII:8130947-8131027 33 2.19e-04 TCTCAGTGAA ATACACTC GCCCACCACA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ACACACWC MEME-3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrIII:4899852-4899932 1.4e-05 35_[+3]_37 chrIII:1925267-1925347 1.4e-05 72_[+3] chrIV:5607487-5607567 1.4e-05 10_[+3]_62 chrV:12537672-12537752 1.4e-05 20_[+3]_52 chrIII:10407471-10407551 2.8e-05 54_[+3]_18 chrX:11478905-11478985 2.8e-05 71_[+3]_1 chrII:11620126-11620206 7.2e-05 9_[+3]_63 chrX:2599035-2599115 0.00012 [+3]_72 chrX:10640613-10640693 0.00012 40_[+3]_32 chrX:17505891-17505971 0.00014 20_[+3]_52 chrX:9958678-9958758 0.00017 4_[+3]_68 chrII:8130947-8131027 0.00022 32_[+3]_40 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ACACACWC MEME-3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF ACACACWC width=8 seqs=12 chrIII:4899852-4899932 ( 36) ACACACAC 1 chrIII:1925267-1925347 ( 73) ACACACAC 1 chrIV:5607487-5607567 ( 11) ACACACAC 1 chrV:12537672-12537752 ( 21) ACACACAC 1 chrIII:10407471-10407551 ( 55) ACACACTC 1 chrX:11478905-11478985 ( 72) ACACACTC 1 chrII:11620126-11620206 ( 10) ACACAGAC 1 chrX:2599035-2599115 ( 1) ACACACAA 1 chrX:10640613-10640693 ( 41) AAACACAC 1 chrX:17505891-17505971 ( 21) ACACACTG 1 chrX:9958678-9958758 ( 5) ACACTCTC 1 chrII:8130947-8131027 ( 33) ATACACTC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ACACACWC MEME-3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 5475 bayes= 9.93174 E= 1.3e+003 187 -1023 -1023 -1023 -171 189 -1023 -171 187 -1023 -1023 -1023 -1023 215 -1023 -1023 175 -1023 -1023 -171 -1023 203 -146 -1023 110 -1023 -1023 61 -171 189 -146 -1023 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ACACACWC MEME-3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 12 E= 1.3e+003 1.000000 0.000000 0.000000 0.000000 0.083333 0.833333 0.000000 0.083333 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.916667 0.000000 0.000000 0.083333 0.000000 0.916667 0.083333 0.000000 0.583333 0.000000 0.000000 0.416667 0.083333 0.833333 0.083333 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ACACACWC MEME-3 regular expression -------------------------------------------------------------------------------- ACACAC[AT]C -------------------------------------------------------------------------------- Time 2.43 secs. ******************************************************************************** ******************************************************************************** MOTIF ATGCACTT MEME-4 width = 8 sites = 11 llr = 102 E-value = 4.2e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif ATGCACTT MEME-4 Description -------------------------------------------------------------------------------- Simplified A a:::9:1: pos.-specific C :::71a:: probability G ::a:::2: matrix T :a:3::7a bits 2.2 * * 1.9 *** * * 1.7 *** * * 1.5 *** ** * Relative 1.3 ****** * Entropy 1.1 ****** * (13.4 bits) 0.9 ******** 0.6 ******** 0.4 ******** 0.2 ******** 0.0 -------- Multilevel ATGCACTT consensus T sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ATGCACTT MEME-4 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chrV:12528355-12528435 33 1.77e-05 GACAGTACAC ATGCACTT TTGGCTCGTT chrIV:8793501-8793581 38 1.77e-05 GTAGGAGTTC ATGCACTT TGAAAAGTGC chrV:14366704-14366784 26 1.77e-05 CGCGTCAGGG ATGCACTT TTATAAAAGT chrII:8130947-8131027 15 1.77e-05 TGCACTTTAA ATGCACTT TCTCAGTGAA chrX:11478905-11478985 41 1.77e-05 CATAGTACAG ATGCACTT TTTTCCAACC chrX:16024800-16024880 27 5.40e-05 CCGTCGAGAC ATGCACGT CAGCGCCGAG chrIII:12841531-12841611 40 5.40e-05 CGACAGAAAA ATGTACTT TCTCGTTCGG chrV:14368801-14368881 54 5.40e-05 AAATAAGTCT ATGTACTT CTGAAAGTAC chrV:12530271-12530351 26 7.16e-05 GATAGAATAA ATGCACAT GCTCACAAGT chrII:1238085-1238165 54 8.62e-05 GTCAGCGATG ATGCCCTT TCATGCACTA chrV:5271594-5271674 65 1.04e-04 TGTTCACGTG ATGTACGT GCAAAAAG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ATGCACTT MEME-4 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrV:12528355-12528435 1.8e-05 32_[+4]_40 chrIV:8793501-8793581 1.8e-05 37_[+4]_35 chrV:14366704-14366784 1.8e-05 25_[+4]_47 chrII:8130947-8131027 1.8e-05 14_[+4]_58 chrX:11478905-11478985 1.8e-05 40_[+4]_32 chrX:16024800-16024880 5.4e-05 26_[+4]_46 chrIII:12841531-12841611 5.4e-05 39_[+4]_33 chrV:14368801-14368881 5.4e-05 53_[+4]_19 chrV:12530271-12530351 7.2e-05 25_[+4]_47 chrII:1238085-1238165 8.6e-05 53_[+4]_19 chrV:5271594-5271674 0.0001 64_[+4]_8 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ATGCACTT MEME-4 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF ATGCACTT width=8 seqs=11 chrV:12528355-12528435 ( 33) ATGCACTT 1 chrIV:8793501-8793581 ( 38) ATGCACTT 1 chrV:14366704-14366784 ( 26) ATGCACTT 1 chrII:8130947-8131027 ( 15) ATGCACTT 1 chrX:11478905-11478985 ( 41) ATGCACTT 1 chrX:16024800-16024880 ( 27) ATGCACGT 1 chrIII:12841531-12841611 ( 40) ATGTACTT 1 chrV:14368801-14368881 ( 54) ATGTACTT 1 chrV:12530271-12530351 ( 26) ATGCACAT 1 chrII:1238085-1238165 ( 54) ATGCCCTT 1 chrV:5271594-5271674 ( 65) ATGTACGT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ATGCACTT MEME-4 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 5475 bayes= 9.31204 E= 4.2e+001 187 -1010 -1010 -1010 -1010 -1010 -1010 187 -1010 -1010 212 -1010 -1010 169 -1010 0 174 -131 -1010 -1010 -1010 215 -1010 -1010 -158 -1010 -34 141 -1010 -1010 -1010 187 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ATGCACTT MEME-4 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 11 E= 4.2e+001 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.727273 0.000000 0.272727 0.909091 0.090909 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.090909 0.000000 0.181818 0.727273 0.000000 0.000000 0.000000 1.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ATGCACTT MEME-4 regular expression -------------------------------------------------------------------------------- ATG[CT]ACTT -------------------------------------------------------------------------------- Time 3.14 secs. ******************************************************************************** ******************************************************************************** MOTIF GCGRSCGC MEME-5 width = 8 sites = 7 llr = 68 E-value = 4.0e+003 ******************************************************************************** -------------------------------------------------------------------------------- Motif GCGRSCGC MEME-5 Description -------------------------------------------------------------------------------- Simplified A :::6:::: pos.-specific C :a114a:a probability G a:936:a: matrix T :::::::: bits 2.2 ** *** 1.9 ** *** 1.7 ** *** 1.5 *** *** Relative 1.3 *** *** Entropy 1.1 *** **** (14.0 bits) 0.9 *** **** 0.6 ******** 0.4 ******** 0.2 ******** 0.0 -------- Multilevel GCGAGCGC consensus GC sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCGRSCGC MEME-5 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chrII:11620126-11620206 43 8.70e-06 AATGAAAAGC GCGAGCGC CCCCAGGCGC chrX:16024800-16024880 10 1.72e-05 GGGCGACGC GCGACCGC CGTCGAGACA chrX:10637620-10637700 31 1.72e-05 AAGCGCAGCA GCGACCGC CGCCGAAAAC chrI:999215-999295 28 2.45e-05 GGTAAGGAAC GCGGGCGC CCGCAAGGAA chrIII:4899852-4899932 48 3.17e-05 ACACACTTTC GCGGCCGC TACGCAGAGA chrIV:4445892-4445972 58 3.89e-05 TCTCTCGTTT GCGCGCGC TTTTGAGAGT chrX:7230546-7230626 26 5.44e-05 TGAGACCAAG GCCAGCGC AGCGGGACAA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCGRSCGC MEME-5 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrII:11620126-11620206 8.7e-06 42_[+5]_30 chrX:16024800-16024880 1.7e-05 9_[+5]_63 chrX:10637620-10637700 1.7e-05 30_[+5]_42 chrI:999215-999295 2.5e-05 27_[+5]_45 chrIII:4899852-4899932 3.2e-05 47_[+5]_25 chrIV:4445892-4445972 3.9e-05 57_[+5]_15 chrX:7230546-7230626 5.4e-05 25_[+5]_47 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCGRSCGC MEME-5 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF GCGRSCGC width=8 seqs=7 chrII:11620126-11620206 ( 43) GCGAGCGC 1 chrX:16024800-16024880 ( 10) GCGACCGC 1 chrX:10637620-10637700 ( 31) GCGACCGC 1 chrI:999215-999295 ( 28) GCGGGCGC 1 chrIII:4899852-4899932 ( 48) GCGGCCGC 1 chrIV:4445892-4445972 ( 58) GCGCGCGC 1 chrX:7230546-7230626 ( 26) GCCAGCGC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCGRSCGC MEME-5 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 5475 bayes= 10.2158 E= 4.0e+003 -945 -945 212 -945 -945 215 -945 -945 -945 -65 190 -945 107 -65 32 -945 -945 93 131 -945 -945 215 -945 -945 -945 -945 212 -945 -945 215 -945 -945 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCGRSCGC MEME-5 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 7 E= 4.0e+003 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.142857 0.857143 0.000000 0.571429 0.142857 0.285714 0.000000 0.000000 0.428571 0.571429 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCGRSCGC MEME-5 regular expression -------------------------------------------------------------------------------- GCG[AG][GC]CGC -------------------------------------------------------------------------------- Time 3.87 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrV:14368801-14368881 3.83e-03 53_[+4(5.40e-05)]_3_[+1(2.14e-05)]_\ 8 chrIII:12841531-12841611 4.14e-05 8_[+2(1.55e-05)]_23_[+4(5.40e-05)]_\ 15_[+1(3.95e-05)]_10 chrV:12529078-12529158 7.92e-01 80 chrX:11478905-11478985 2.57e-05 40_[+4(1.77e-05)]_23_[+3(2.85e-05)]_\ 1 chrII:8130947-8131027 1.15e-03 14_[+4(1.77e-05)]_58 chrV:14366704-14366784 5.76e-04 25_[+4(1.77e-05)]_5_[+1(2.14e-05)]_\ 34 chrX:11482321-11482401 1.73e-03 56_[+1(3.95e-05)]_16 chrV:12537672-12537752 3.08e-02 20_[+3(1.42e-05)]_52 chrI:14620901-14620981 9.91e-01 80 chrII:11619287-11619367 2.70e-03 71_[+1(3.95e-05)]_1 chrII:1238085-1238165 6.88e-03 20_[+2(8.40e-05)]_25_[+4(8.62e-05)]_\ 19 chrIV:8793501-8793581 3.25e-03 37_[+4(1.77e-05)]_3_[+1(3.95e-05)]_\ 24 chrV:12540106-12540186 8.71e-01 80 chrX:535881-535961 1.86e-02 80 chrX:7230546-7230626 1.33e-02 25_[+5(5.44e-05)]_47 chrIV:11063222-11063302 9.98e-01 80 chrV:11733596-11733676 4.94e-02 72_[+1(2.14e-05)] chrX:14334310-14334390 9.71e-01 80 chrIII:9766319-9766399 8.05e-01 80 chrI:1691195-1691275 3.49e-02 80 chrX:14561703-14561783 2.40e-02 7_[+1(3.95e-05)]_65 chrIV:5607487-5607567 1.84e-02 6_[+3(1.42e-05)]_66 chrV:12528355-12528435 1.22e-04 23_[+1(8.97e-05)]_1_[+4(1.77e-05)]_\ 40 chrX:5653913-5653993 1.01e-01 22_[+1(7.20e-05)]_50 chrV:12530271-12530351 4.44e-02 25_[+4(7.16e-05)]_47 chrIII:12849378-12849458 1.02e-03 3_[+2(1.55e-05)]_34_[+1(2.14e-05)]_\ 27 chrI:999215-999295 1.09e-04 27_[+5(2.45e-05)]_10_[+1(3.95e-05)]_\ 27 chrV:12533905-12533985 8.36e-01 80 chrX:10640613-10640693 1.28e-01 80 chrII:11620126-11620206 4.56e-07 9_[+3(7.18e-05)]_1_[+2(3.40e-05)]_\ 16_[+5(8.70e-06)]_13_[+1(5.71e-05)]_9 chrIV:14033149-14033229 8.58e-01 80 chrIII:4195284-4195364 5.70e-01 80 chrV:5523307-5523387 1.03e-01 17_[+1(5.71e-05)]_55 chrX:10637620-10637700 6.53e-02 30_[+5(1.72e-05)]_42 chrX:16024800-16024880 5.60e-06 9_[+5(1.72e-05)]_9_[+4(5.40e-05)]_\ 35_[+1(2.14e-05)]_3 chrII:9617859-9617939 3.49e-02 20_[+2(8.40e-05)]_52 chrIV:1070530-1070610 2.43e-02 66_[+2(1.55e-05)]_6 chrIII:4568733-4568813 6.48e-01 80 chrV:14347329-14347409 6.78e-01 80 chrV:265214-265294 6.91e-01 80 chrIV:8529107-8529187 9.53e-01 80 chrV:5271594-5271674 8.69e-02 80 chrV:11147998-11148078 8.28e-01 80 chrIV:9511286-9511366 4.25e-01 80 chrX:12363095-12363175 5.18e-01 80 chrI:8786935-8787015 9.67e-02 80 chrIV:15472549-15472629 9.27e-02 80 chrIII:10407471-10407551 6.29e-03 54_[+3(2.85e-05)]_18 chrX:11465368-11465448 4.47e-01 80 chrX:2364899-2364979 9.49e-01 80 chrX:16056567-16056647 1.38e-01 80 chrX:17505891-17505971 4.53e-03 80 chrI:9343953-9344033 1.73e-01 5_[+2(5.24e-05)]_67 chrI:9422263-9422343 2.93e-01 80 chrIV:14033361-14033441 9.11e-01 80 chrX:2599035-2599115 9.38e-02 80 chrI:397908-397988 8.58e-01 80 chrII:2974025-2974105 2.04e-03 35_[+2(5.24e-05)]_10_[+2(1.55e-05)]_\ 19 chrI:6835315-6835395 2.45e-02 71_[+1(2.14e-05)]_1 chrX:1344968-1345048 6.58e-01 80 chrX:827689-827769 9.40e-01 80 chrII:6951524-6951604 6.97e-01 80 chrV:15766381-15766461 4.44e-01 80 chrIII:5679104-5679184 2.16e-02 80 chrII:12944658-12944738 7.29e-01 80 chrIII:12612640-12612720 9.95e-01 80 chrX:9958678-9958758 1.47e-01 80 chrIII:1925267-1925347 4.12e-02 72_[+3(1.42e-05)] chrIV:4445892-4445972 1.21e-01 57_[+5(3.89e-05)]_15 chrX:5841221-5841301 6.15e-01 80 chrIII:8795851-8795931 1.57e-02 42_[+2(5.24e-05)]_30 chrIV:8795161-8795241 4.89e-02 3_[+2(5.24e-05)]_69 chrIII:4899852-4899932 8.76e-04 35_[+3(1.42e-05)]_4_[+5(3.17e-05)]_\ 25 chrII:3077095-3077175 8.77e-02 80 chrIV:8527820-8527900 1.20e-01 80 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (5) found. ******************************************************************************** CPU: c27n09.farnam.hpc.yale.internal ********************************************************************************