******************************************************************************** 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/unc-62.fasta CONTROL SEQUENCES= --none-- ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ chrIV:13695878-13695958 1.0000 80 chrV:4508253-4508333 1.0000 80 chrV:4508054-4508134 1.0000 80 chrIII:6979161-6979241 1.0000 80 chrIV:11068485-11068565 1.0000 80 chrI:3121739-3121819 1.0000 80 chrX:15600013-15600093 1.0000 80 chrX:13329061-13329141 1.0000 80 chrI:9097777-9097857 1.0000 80 chrIII:11935795-11935875 1.0000 80 chrIII:8021116-8021196 1.0000 80 chrIV:13704216-13704296 1.0000 80 chrX:10147357-10147437 1.0000 80 chrV:4495202-4495282 1.0000 80 chrV:20781889-20781969 1.0000 80 chrV:7746117-7746197 1.0000 80 chrV:13086017-13086097 1.0000 80 chrI:8590644-8590724 1.0000 80 chrIII:1926596-1926676 1.0000 80 chrIII:1923674-1923754 1.0000 80 chrII:7839005-7839085 1.0000 80 chrX:12393971-12394051 1.0000 80 chrV:16965817-16965897 1.0000 80 chrII:10851344-10851424 1.0000 80 chrII:13447778-13447858 1.0000 80 chrV:13081431-13081511 1.0000 80 chrII:2974024-2974104 1.0000 80 chrIII:8800163-8800243 1.0000 80 chrI:7128379-7128459 1.0000 80 chrI:535408-535488 1.0000 80 chrII:4299394-4299474 1.0000 80 chrII:11642123-11642203 1.0000 80 chrIV:5593987-5594067 1.0000 80 chrX:1446909-1446989 1.0000 80 chrII:10868937-10869017 1.0000 80 chrIII:12273627-12273707 1.0000 80 chrI:9163486-9163566 1.0000 80 chrI:3266718-3266798 1.0000 80 chrV:9546971-9547051 1.0000 80 chrV:9175465-9175545 1.0000 80 chrI:8329750-8329830 1.0000 80 chrV:19522907-19522987 1.0000 80 chrIII:4223806-4223886 1.0000 80 chrV:10715969-10716049 1.0000 80 chrIII:3460225-3460305 1.0000 80 chrIV:15471580-15471660 1.0000 80 chrIV:5183820-5183900 1.0000 80 chrIII:1925388-1925468 1.0000 80 chrIII:5679078-5679158 1.0000 80 chrIII:12612629-12612709 1.0000 80 chrX:5841270-5841350 1.0000 80 chrIV:443782-443862 1.0000 80 chrII:9282949-9283029 1.0000 80 chrII:6331559-6331639 1.0000 80 chrIII:13061262-13061342 1.0000 80 chrV:14685710-14685790 1.0000 80 chrII:8185169-8185249 1.0000 80 chrX:6744128-6744208 1.0000 80 chrIII:6972067-6972147 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_unc-62/ -dna -nmotifs 5 -w 8 -maxsize 250000 -nostatus ../result/final_prediction/worm/fasta/RankLinear2.0_40/unc-62.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= 59 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= 4720 N= 59 sample: seed= 0 hsfrac= 0 searchsize= 4720 norand= no csites= 1000 Letter frequencies in dataset: A 0.26 C 0.227 G 0.236 T 0.277 Background letter frequencies (from file dataset with add-one prior applied): A 0.26 C 0.227 G 0.236 T 0.277 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF RAAAAGAG MEME-1 width = 8 sites = 16 llr = 132 E-value = 4.9e+000 ******************************************************************************** -------------------------------------------------------------------------------- Motif RAAAAGAG MEME-1 Description -------------------------------------------------------------------------------- Simplified A 49a79:8: pos.-specific C :1:::::1 probability G 6::3:a19 matrix T ::::1:1: 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 GAAAAGAG consensus A G sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RAAAAGAG MEME-1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chrX:1446909-1446989 56 1.56e-05 GGTGGCGAGG GAAAAGAG GCACGAGACG chrI:9097777-9097857 23 1.56e-05 ATTTCAGATT GAAAAGAG AGGAAAAAAC chrV:4508253-4508333 36 1.56e-05 AATTTATGAG GAAAAGAG TGATTGCTTT chrIII:4223806-4223886 45 3.28e-05 GACGACAAAA AAAAAGAG TTATGGAGAA chrI:535408-535488 66 3.28e-05 GTCATATAGC AAAAAGAG AAACACC chrI:8590644-8590724 31 3.28e-05 CCTCTTCAAC AAAAAGAG TGACGACAAG chrIV:11068485-11068565 25 4.70e-05 TTTCAATGTT GAAGAGAG ATACGTGTGT chrV:4508054-4508134 25 4.70e-05 TATAGAGTAA GAAGAGAG TGGAAAGAGG chrV:14685710-14685790 73 9.04e-05 ATTTTCCGCC GAAAAGGG chrIV:5183820-5183900 35 9.04e-05 CGGAAAACGC GCAAAGAG CGAGAGCTGA chrX:10147357-10147437 44 1.38e-04 CAAATAAATC AAAAAGGG AAATTGAAGA chrII:9282949-9283029 39 1.81e-04 AAGAGCATGT AAAAAGTG GAGACTCGAG chrII:2974024-2974104 50 1.96e-04 AGAGAGCGTG GAAGAGTG AGAGAGCGCG chrI:7128379-7128459 47 2.28e-04 GTGTAGCGCT GAAATGAG AGAAACACTC chrIII:13061262-13061342 2 2.56e-04 G ACAGAGAG CGCATTAAGA chrII:4299394-4299474 64 3.21e-04 GTCTCGCAGG GAAGAGAC GACGCGGGG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RAAAAGAG MEME-1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrX:1446909-1446989 1.6e-05 55_[+1]_17 chrI:9097777-9097857 1.6e-05 22_[+1]_50 chrV:4508253-4508333 1.6e-05 35_[+1]_37 chrIII:4223806-4223886 3.3e-05 44_[+1]_28 chrI:535408-535488 3.3e-05 65_[+1]_7 chrI:8590644-8590724 3.3e-05 30_[+1]_42 chrIV:11068485-11068565 4.7e-05 24_[+1]_48 chrV:4508054-4508134 4.7e-05 24_[+1]_48 chrV:14685710-14685790 9e-05 72_[+1] chrIV:5183820-5183900 9e-05 34_[+1]_38 chrX:10147357-10147437 0.00014 43_[+1]_29 chrII:9282949-9283029 0.00018 38_[+1]_34 chrII:2974024-2974104 0.0002 49_[+1]_23 chrI:7128379-7128459 0.00023 46_[+1]_26 chrIII:13061262-13061342 0.00026 1_[+1]_71 chrII:4299394-4299474 0.00032 63_[+1]_9 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RAAAAGAG MEME-1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF RAAAAGAG width=8 seqs=16 chrX:1446909-1446989 ( 56) GAAAAGAG 1 chrI:9097777-9097857 ( 23) GAAAAGAG 1 chrV:4508253-4508333 ( 36) GAAAAGAG 1 chrIII:4223806-4223886 ( 45) AAAAAGAG 1 chrI:535408-535488 ( 66) AAAAAGAG 1 chrI:8590644-8590724 ( 31) AAAAAGAG 1 chrIV:11068485-11068565 ( 25) GAAGAGAG 1 chrV:4508054-4508134 ( 25) GAAGAGAG 1 chrV:14685710-14685790 ( 73) GAAAAGGG 1 chrIV:5183820-5183900 ( 35) GCAAAGAG 1 chrX:10147357-10147437 ( 44) AAAAAGGG 1 chrII:9282949-9283029 ( 39) AAAAAGTG 1 chrII:2974024-2974104 ( 50) GAAGAGTG 1 chrI:7128379-7128459 ( 47) GAAATGAG 1 chrIII:13061262-13061342 ( 2) ACAGAGAG 1 chrII:4299394-4299474 ( 64) GAAGAGAC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RAAAAGAG MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 4307 bayes= 8.0671 E= 4.9e+000 53 -1064 140 -1064 175 -86 -1064 -1064 195 -1064 -1064 -1064 140 -1064 40 -1064 185 -1064 -1064 -214 -1064 -1064 208 -1064 153 -1064 -92 -115 -1064 -186 199 -1064 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RAAAAGAG MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 16 E= 4.9e+000 0.375000 0.000000 0.625000 0.000000 0.875000 0.125000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.687500 0.000000 0.312500 0.000000 0.937500 0.000000 0.000000 0.062500 0.000000 0.000000 1.000000 0.000000 0.750000 0.000000 0.125000 0.125000 0.000000 0.062500 0.937500 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RAAAAGAG MEME-1 regular expression -------------------------------------------------------------------------------- [GA]AA[AG]AGAG -------------------------------------------------------------------------------- Time 0.89 secs. ******************************************************************************** ******************************************************************************** MOTIF CDTTTTTC MEME-2 width = 8 sites = 34 llr = 227 E-value = 3.2e-002 ******************************************************************************** -------------------------------------------------------------------------------- Motif CDTTTTTC MEME-2 Description -------------------------------------------------------------------------------- Simplified A :411:::: pos.-specific C a:3:2::9 probability G :3:1:2:: matrix T :36788a1 bits 2.1 * 1.9 * 1.7 * ** 1.5 * ** Relative 1.3 * **** Entropy 1.1 * **** (9.6 bits) 0.9 * **** 0.6 * ****** 0.4 ******** 0.2 ******** 0.0 -------- Multilevel CATTTTTC consensus GC C sequence T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CDTTTTTC MEME-2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chrIV:443782-443862 15 2.18e-05 TAATTTCTCG CATTTTTC TCATTTCTTA chrIII:1926596-1926676 68 2.18e-05 GTCTTTCGCC CATTTTTC CTTTT chrII:11642123-11642203 54 4.17e-05 TGATAAATCA CGTTTTTC GTCCGTTTCT chrII:13447778-13447858 48 4.17e-05 AAATATCAGC CGTTTTTC TTCATCAGCT chrV:9175465-9175545 24 8.29e-05 tcttttctca cttttttc ttcAAAAAAC chrII:7839005-7839085 37 8.29e-05 CAATGTGTGT CACTTTTC ATTAAAATAT chrI:8590644-8590724 7 8.29e-05 CCAACT CTTTTTTC TCTGCGCCTC chrIII:6979161-6979241 54 8.29e-05 GTATATCCAT CTTTTTTC GAGACGTTTT chrV:4508253-4508333 50 8.29e-05 AGAGTGATTG CTTTTTTC GGCGGTTTTC chrV:9546971-9547051 22 9.91e-05 GTTTCTGTGA CGCTTTTC TGACATGTGT chrX:6744128-6744208 25 1.36e-04 CAATCGTACT CATTCTTC TTCCAATGTG chrV:14685710-14685790 48 1.57e-04 GCTCTATTGA CAATTTTC GTCGAGAATT chrIII:1923674-1923754 30 1.94e-04 CAACCTCACT CATTTGTC TTCTGATGGA chrX:15600013-15600093 68 1.94e-04 ATGAAGCTGT CATTTGTC CATTC chrIV:15471580-15471660 72 2.83e-04 GATTTGTTGA CGTGTTTC T chrIV:5593987-5594067 60 4.27e-04 CAAACAACAA CTTTTGTC TTTTGCCTCT chrIII:11935795-11935875 12 4.27e-04 GGGTTTGAGT CACTTGTC AAGACTCTAC chrIII:5679078-5679158 45 4.79e-04 CGCTCTATAG CACATTTC ACTGTGCCGC chrII:6331559-6331639 41 5.07e-04 CCGGGCAGAT CGCGTTTC GTGCCTTGGT chrIV:5183820-5183900 53 5.38e-04 CGAGAGCTGA CGCATTTC GCGACTCGTA chrIII:3460225-3460305 73 5.38e-04 CATGTGCTGG CGCATTTC chrI:9097777-9097857 67 5.38e-04 CTCTGTCACT CTCTCTTC TTGATG chrV:13081431-13081511 39 5.55e-04 GCAAGGTCAT CAATCTTC TGCAACAGGA chrIV:13695878-13695958 18 5.55e-04 CATGAGTAAT CAATCTTC GTTGCAAGAC chrIII:12273627-12273707 51 6.44e-04 CGATATCTCG CATTTTTT CATGGAAAAT chrI:3121739-3121819 17 6.44e-04 AATTTCATCA CATTTTTT CAAGAATCTC chrI:8329750-8329830 6 7.64e-04 AAGTA CAAATTTC GTAGGAGGGT chrV:16965817-16965897 71 7.64e-04 CGCTTGCACT CAAATTTC CG chrIII:8800163-8800243 11 8.34e-04 AGGAGGTCCG CGTGCTTC cacatacaca chrV:4508054-4508134 69 8.34e-04 cacacaGGGA CGTGCTTC GGAT chrIV:11068485-11068565 36 9.31e-04 AAGAGAGATA CGTGTGTC ACATGATTAG chrV:4495202-4495282 73 1.05e-03 ATTCTCCTTC CTTTTTTT chrX:13329061-13329141 3 1.39e-03 CT CTCTCGTC AGTGCAAATA chrV:13086017-13086097 44 1.67e-03 GAGTTGGCGT CTTTTTCC CCACTTTCGG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CDTTTTTC MEME-2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrIV:443782-443862 2.2e-05 14_[+2]_58 chrIII:1926596-1926676 2.2e-05 67_[+2]_5 chrII:11642123-11642203 4.2e-05 53_[+2]_19 chrII:13447778-13447858 4.2e-05 47_[+2]_25 chrV:9175465-9175545 8.3e-05 23_[+2]_49 chrII:7839005-7839085 8.3e-05 36_[+2]_36 chrI:8590644-8590724 8.3e-05 6_[+2]_66 chrIII:6979161-6979241 8.3e-05 53_[+2]_19 chrV:4508253-4508333 8.3e-05 49_[+2]_23 chrV:9546971-9547051 9.9e-05 21_[+2]_51 chrX:6744128-6744208 0.00014 24_[+2]_48 chrV:14685710-14685790 0.00016 47_[+2]_25 chrIII:1923674-1923754 0.00019 29_[+2]_43 chrX:15600013-15600093 0.00019 67_[+2]_5 chrIV:15471580-15471660 0.00028 71_[+2]_1 chrIV:5593987-5594067 0.00043 59_[+2]_13 chrIII:11935795-11935875 0.00043 11_[+2]_61 chrIII:5679078-5679158 0.00048 44_[+2]_28 chrII:6331559-6331639 0.00051 40_[+2]_32 chrIV:5183820-5183900 0.00054 52_[+2]_20 chrIII:3460225-3460305 0.00054 72_[+2] chrI:9097777-9097857 0.00054 66_[+2]_6 chrV:13081431-13081511 0.00055 38_[+2]_34 chrIV:13695878-13695958 0.00055 17_[+2]_55 chrIII:12273627-12273707 0.00064 50_[+2]_22 chrI:3121739-3121819 0.00064 16_[+2]_56 chrI:8329750-8329830 0.00076 5_[+2]_67 chrV:16965817-16965897 0.00076 70_[+2]_2 chrIII:8800163-8800243 0.00083 10_[+2]_62 chrV:4508054-4508134 0.00083 68_[+2]_4 chrIV:11068485-11068565 0.00093 35_[+2]_37 chrV:4495202-4495282 0.0011 72_[+2] chrX:13329061-13329141 0.0014 2_[+2]_70 chrV:13086017-13086097 0.0017 43_[+2]_29 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CDTTTTTC MEME-2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF CDTTTTTC width=8 seqs=34 chrIV:443782-443862 ( 15) CATTTTTC 1 chrIII:1926596-1926676 ( 68) CATTTTTC 1 chrII:11642123-11642203 ( 54) CGTTTTTC 1 chrII:13447778-13447858 ( 48) CGTTTTTC 1 chrV:9175465-9175545 ( 24) CTTTTTTC 1 chrII:7839005-7839085 ( 37) CACTTTTC 1 chrI:8590644-8590724 ( 7) CTTTTTTC 1 chrIII:6979161-6979241 ( 54) CTTTTTTC 1 chrV:4508253-4508333 ( 50) CTTTTTTC 1 chrV:9546971-9547051 ( 22) CGCTTTTC 1 chrX:6744128-6744208 ( 25) CATTCTTC 1 chrV:14685710-14685790 ( 48) CAATTTTC 1 chrIII:1923674-1923754 ( 30) CATTTGTC 1 chrX:15600013-15600093 ( 68) CATTTGTC 1 chrIV:15471580-15471660 ( 72) CGTGTTTC 1 chrIV:5593987-5594067 ( 60) CTTTTGTC 1 chrIII:11935795-11935875 ( 12) CACTTGTC 1 chrIII:5679078-5679158 ( 45) CACATTTC 1 chrII:6331559-6331639 ( 41) CGCGTTTC 1 chrIV:5183820-5183900 ( 53) CGCATTTC 1 chrIII:3460225-3460305 ( 73) CGCATTTC 1 chrI:9097777-9097857 ( 67) CTCTCTTC 1 chrV:13081431-13081511 ( 39) CAATCTTC 1 chrIV:13695878-13695958 ( 18) CAATCTTC 1 chrIII:12273627-12273707 ( 51) CATTTTTT 1 chrI:3121739-3121819 ( 17) CATTTTTT 1 chrI:8329750-8329830 ( 6) CAAATTTC 1 chrV:16965817-16965897 ( 71) CAAATTTC 1 chrIII:8800163-8800243 ( 11) CGTGCTTC 1 chrV:4508054-4508134 ( 69) CGTGCTTC 1 chrIV:11068485-11068565 ( 36) CGTGTGTC 1 chrV:4495202-4495282 ( 73) CTTTTTTT 1 chrX:13329061-13329141 ( 3) CTCTCGTC 1 chrV:13086017-13086097 ( 44) CTTTTTCC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CDTTTTTC MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 4307 bayes= 7.04365 E= 3.2e-002 -1173 214 -1173 -1173 77 -1173 31 -6 -82 22 -1173 109 -82 -1173 -68 135 -1173 -14 -1173 152 -1173 -1173 -42 157 -1173 -295 -1173 181 -1173 200 -1173 -165 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CDTTTTTC MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 34 E= 3.2e-002 0.000000 1.000000 0.000000 0.000000 0.441176 0.000000 0.294118 0.264706 0.147059 0.264706 0.000000 0.588235 0.147059 0.000000 0.147059 0.705882 0.000000 0.205882 0.000000 0.794118 0.000000 0.000000 0.176471 0.823529 0.000000 0.029412 0.000000 0.970588 0.000000 0.911765 0.000000 0.088235 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CDTTTTTC MEME-2 regular expression -------------------------------------------------------------------------------- C[AGT][TC]T[TC]TTC -------------------------------------------------------------------------------- Time 1.54 secs. ******************************************************************************** ******************************************************************************** MOTIF GACGCMRA MEME-3 width = 8 sites = 15 llr = 125 E-value = 1.2e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif GACGCMRA MEME-3 Description -------------------------------------------------------------------------------- Simplified A :a:1373a pos.-specific C ::a173:: probability G 9::7::7: matrix T 1::1:::: bits 2.1 * 1.9 ** * 1.7 *** * 1.5 *** * Relative 1.3 *** * * Entropy 1.1 *** **** (12.0 bits) 0.9 ******** 0.6 ******** 0.4 ******** 0.2 ******** 0.0 -------- Multilevel GACGCAGA consensus ACA sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GACGCMRA MEME-3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chrIV:15471580-15471660 35 1.19e-05 GAGAGTACGA GACGCAGA GATCGTTGGC chrIII:3460225-3460305 12 1.19e-05 AAAGCATGGA GACGCAGA CACGCACGAA chrV:19522907-19522987 4 1.19e-05 GGA GACGCAGA TGGTTAGACG chrV:16965817-16965897 32 1.19e-05 GAAAGGTGGA GACGCAGA CGAGAAAGGT chrV:7746117-7746197 14 2.23e-05 AAGATGAAGA GACGCCGA CGTTTCGAGT chrI:8329750-8329830 64 3.54e-05 GGCAATGATT GACGCAAA TATTGTTCA chrX:1446909-1446989 70 7.24e-05 AGAGGCACGA GACGACGA GAG chrV:4508253-4508333 68 7.24e-05 GGCGGTTTTC GACGACGA GACTT chrV:13086017-13086097 17 1.13e-04 TGCCCTGCCG GACCCAGA AGCAGCGGTG chrV:20781889-20781969 42 1.38e-04 ACGTGGCGAG GACACAGA CACCACCGGC chrIII:4223806-4223886 35 1.51e-04 GAGATGGGAG GACGACAA AAAAAAAGAG chrI:8590644-8590724 40 1.51e-04 CAAAAAGAGT GACGACAA GGCGATTTCT chrX:5841270-5841350 63 1.67e-04 GGTGTGTAGC GACTCAAA CGGCCGGCGT chrIII:5679078-5679158 63 1.67e-04 ACTGTGCCGC GACTCAAA GACATGCTGC chrIII:13061262-13061342 39 1.81e-04 GGAGATGAGA TACGCAGA GAAGCATACA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GACGCMRA MEME-3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrIV:15471580-15471660 1.2e-05 34_[+3]_38 chrIII:3460225-3460305 1.2e-05 11_[+3]_61 chrV:19522907-19522987 1.2e-05 3_[+3]_69 chrV:16965817-16965897 1.2e-05 31_[+3]_41 chrV:7746117-7746197 2.2e-05 13_[+3]_59 chrI:8329750-8329830 3.5e-05 63_[+3]_9 chrX:1446909-1446989 7.2e-05 69_[+3]_3 chrV:4508253-4508333 7.2e-05 67_[+3]_5 chrV:13086017-13086097 0.00011 16_[+3]_56 chrV:20781889-20781969 0.00014 41_[+3]_31 chrIII:4223806-4223886 0.00015 34_[+3]_38 chrI:8590644-8590724 0.00015 39_[+3]_33 chrX:5841270-5841350 0.00017 62_[+3]_10 chrIII:5679078-5679158 0.00017 62_[+3]_10 chrIII:13061262-13061342 0.00018 38_[+3]_34 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GACGCMRA MEME-3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF GACGCMRA width=8 seqs=15 chrIV:15471580-15471660 ( 35) GACGCAGA 1 chrIII:3460225-3460305 ( 12) GACGCAGA 1 chrV:19522907-19522987 ( 4) GACGCAGA 1 chrV:16965817-16965897 ( 32) GACGCAGA 1 chrV:7746117-7746197 ( 14) GACGCCGA 1 chrI:8329750-8329830 ( 64) GACGCAAA 1 chrX:1446909-1446989 ( 70) GACGACGA 1 chrV:4508253-4508333 ( 68) GACGACGA 1 chrV:13086017-13086097 ( 17) GACCCAGA 1 chrV:20781889-20781969 ( 42) GACACAGA 1 chrIII:4223806-4223886 ( 35) GACGACAA 1 chrI:8590644-8590724 ( 40) GACGACAA 1 chrX:5841270-5841350 ( 63) GACTCAAA 1 chrIII:5679078-5679158 ( 63) GACTCAAA 1 chrIII:13061262-13061342 ( 39) TACGCAGA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GACGCMRA MEME-3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 4307 bayes= 8.83665 E= 1.2e+001 -1055 -1055 198 -205 195 -1055 -1055 -1055 -1055 214 -1055 -1055 -196 -177 163 -105 4 169 -1055 -1055 136 55 -1055 -1055 36 -1055 149 -1055 195 -1055 -1055 -1055 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GACGCMRA MEME-3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 15 E= 1.2e+001 0.000000 0.000000 0.933333 0.066667 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.066667 0.066667 0.733333 0.133333 0.266667 0.733333 0.000000 0.000000 0.666667 0.333333 0.000000 0.000000 0.333333 0.000000 0.666667 0.000000 1.000000 0.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GACGCMRA MEME-3 regular expression -------------------------------------------------------------------------------- GACG[CA][AC][GA]A -------------------------------------------------------------------------------- Time 2.16 secs. ******************************************************************************** ******************************************************************************** MOTIF GCGCTCTA MEME-4 width = 8 sites = 5 llr = 51 E-value = 5.4e+003 ******************************************************************************** -------------------------------------------------------------------------------- Motif GCGCTCTA MEME-4 Description -------------------------------------------------------------------------------- Simplified A :::::::8 pos.-specific C :a:a:a:2 probability G a:8::::: matrix T ::2:a:a: bits 2.1 ** * * 1.9 ** **** 1.7 ** **** 1.5 ** **** Relative 1.3 ******** Entropy 1.1 ******** (14.8 bits) 0.9 ******** 0.6 ******** 0.4 ******** 0.2 ******** 0.0 -------- Multilevel GCGCTCTA consensus T C sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCGCTCTA MEME-4 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chrV:14685710-14685790 36 1.30e-05 TGCTGAAAAC GCGCTCTA TTGACAATTT chrIII:5679078-5679158 34 1.30e-05 AATGGCAAGC GCGCTCTA TAGCACATTT chrIV:15471580-15471660 4 1.30e-05 AGT GCGCTCTA TCTGCACGCC chrI:9163486-9163566 22 1.30e-05 gtttgaattg gcgctcta ccgtactttg chrIII:8021116-8021196 35 5.29e-05 CGTTTGCTAC GCTCTCTC GCCGAACAAG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCGCTCTA MEME-4 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrV:14685710-14685790 1.3e-05 35_[+4]_37 chrIII:5679078-5679158 1.3e-05 33_[+4]_39 chrIV:15471580-15471660 1.3e-05 3_[+4]_69 chrI:9163486-9163566 1.3e-05 21_[+4]_51 chrIII:8021116-8021196 5.3e-05 34_[+4]_38 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCGCTCTA MEME-4 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF GCGCTCTA width=8 seqs=5 chrV:14685710-14685790 ( 36) GCGCTCTA 1 chrIII:5679078-5679158 ( 34) GCGCTCTA 1 chrIV:15471580-15471660 ( 4) GCGCTCTA 1 chrI:9163486-9163566 ( 22) GCGCTCTA 1 chrIII:8021116-8021196 ( 35) GCTCTCTC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCGCTCTA MEME-4 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 4307 bayes= 10.0007 E= 5.4e+003 -897 -897 208 -897 -897 214 -897 -897 -897 -897 176 -47 -897 214 -897 -897 -897 -897 -897 185 -897 214 -897 -897 -897 -897 -897 185 162 -18 -897 -897 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCGCTCTA MEME-4 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 5 E= 5.4e+003 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.800000 0.200000 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 0.000000 0.000000 1.000000 0.800000 0.200000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCGCTCTA MEME-4 regular expression -------------------------------------------------------------------------------- GC[GT]CTCT[AC] -------------------------------------------------------------------------------- Time 2.80 secs. ******************************************************************************** ******************************************************************************** MOTIF CTCYCCCC MEME-5 width = 8 sites = 2 llr = 22 E-value = 1.2e+004 ******************************************************************************** -------------------------------------------------------------------------------- Motif CTCYCCCC MEME-5 Description -------------------------------------------------------------------------------- Simplified A :::::::: pos.-specific C a:a5aaaa probability G :::::::: matrix T :a:5:::: bits 2.1 * * **** 1.9 *** **** 1.7 *** **** 1.5 *** **** Relative 1.3 *** **** Entropy 1.1 ******** (15.7 bits) 0.9 ******** 0.6 ******** 0.4 ******** 0.2 ******** 0.0 -------- Multilevel CTCCCCCC consensus T sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTCYCCCC MEME-5 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chrIII:6979161-6979241 22 8.60e-06 CGTTCGACGT CTCCCCCC AACGTCGTTT chrIII:6972067-6972147 4 1.91e-05 AAT CTCTCCCC CTCTCGTTGC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTCYCCCC MEME-5 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrIII:6979161-6979241 8.6e-06 21_[+5]_51 chrIII:6972067-6972147 1.9e-05 3_[+5]_69 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTCYCCCC MEME-5 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF CTCYCCCC width=8 seqs=2 chrIII:6979161-6979241 ( 22) CTCCCCCC 1 chrIII:6972067-6972147 ( 4) CTCTCCCC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTCYCCCC MEME-5 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 4307 bayes= 11.0718 E= 1.2e+004 -765 213 -765 -765 -765 -765 -765 185 -765 213 -765 -765 -765 113 -765 85 -765 213 -765 -765 -765 213 -765 -765 -765 213 -765 -765 -765 213 -765 -765 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTCYCCCC MEME-5 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 2 E= 1.2e+004 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 0.500000 0.000000 0.500000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTCYCCCC MEME-5 regular expression -------------------------------------------------------------------------------- CTC[CT]CCCC -------------------------------------------------------------------------------- Time 3.37 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrIV:13695878-13695958 5.19e-01 80 chrV:4508253-4508333 1.33e-04 35_[+1(1.56e-05)]_6_[+2(8.29e-05)]_\ 10_[+3(7.24e-05)]_5 chrV:4508054-4508134 2.96e-02 24_[+1(4.70e-05)]_48 chrIII:6979161-6979241 4.51e-03 21_[+5(8.60e-06)]_24_[+2(8.29e-05)]_\ 19 chrIV:11068485-11068565 6.65e-02 24_[+1(4.70e-05)]_48 chrI:3121739-3121819 5.01e-01 80 chrX:15600013-15600093 1.49e-01 80 chrX:13329061-13329141 1.44e-01 80 chrI:9097777-9097857 5.45e-04 22_[+1(1.56e-05)]_50 chrIII:11935795-11935875 3.48e-01 80 chrIII:8021116-8021196 1.25e-02 34_[+4(5.29e-05)]_38 chrIV:13704216-13704296 5.93e-01 80 chrX:10147357-10147437 8.47e-02 80 chrV:4495202-4495282 3.06e-01 80 chrV:20781889-20781969 2.30e-01 80 chrV:7746117-7746197 1.43e-02 13_[+3(2.23e-05)]_59 chrV:13086017-13086097 4.00e-02 80 chrI:8590644-8590724 2.66e-05 6_[+2(8.29e-05)]_16_[+1(3.28e-05)]_\ 42 chrIII:1926596-1926676 5.64e-03 67_[+2(2.18e-05)]_5 chrIII:1923674-1923754 8.16e-02 80 chrII:7839005-7839085 2.12e-02 36_[+2(8.29e-05)]_36 chrX:12393971-12394051 5.97e-01 80 chrV:16965817-16965897 8.59e-04 31_[+3(1.19e-05)]_41 chrII:10851344-10851424 3.09e-01 80 chrII:13447778-13447858 1.44e-01 47_[+2(4.17e-05)]_25 chrV:13081431-13081511 4.62e-01 80 chrII:2974024-2974104 4.62e-01 80 chrIII:8800163-8800243 2.20e-01 80 chrI:7128379-7128459 2.02e-01 80 chrI:535408-535488 1.76e-02 65_[+1(3.28e-05)]_7 chrII:4299394-4299474 3.52e-02 80 chrII:11642123-11642203 6.24e-02 53_[+2(4.17e-05)]_19 chrIV:5593987-5594067 4.49e-02 80 chrX:1446909-1446989 3.63e-03 55_[+1(1.56e-05)]_6_[+3(7.24e-05)]_\ 3 chrII:10868937-10869017 1.24e-01 80 chrIII:12273627-12273707 3.77e-01 80 chrI:9163486-9163566 1.01e-02 21_[+4(1.30e-05)]_51 chrI:3266718-3266798 5.21e-01 80 chrV:9546971-9547051 1.30e-02 21_[+2(9.91e-05)]_51 chrV:9175465-9175545 1.11e-01 23_[+2(8.29e-05)]_49 chrI:8329750-8329830 3.67e-02 63_[+3(3.54e-05)]_9 chrV:19522907-19522987 4.10e-02 3_[+3(1.19e-05)]_69 chrIII:4223806-4223886 6.86e-03 44_[+1(3.28e-05)]_28 chrV:10715969-10716049 7.67e-01 80 chrIII:3460225-3460305 1.85e-03 11_[+3(1.19e-05)]_61 chrIV:15471580-15471660 1.71e-05 3_[+4(1.30e-05)]_23_[+3(1.19e-05)]_\ 38 chrIV:5183820-5183900 3.40e-02 34_[+1(9.04e-05)]_38 chrIII:1925388-1925468 1.83e-01 80 chrIII:5679078-5679158 4.88e-04 33_[+4(1.30e-05)]_39 chrIII:12612629-12612709 5.80e-01 80 chrX:5841270-5841350 2.26e-02 80 chrIV:443782-443862 3.20e-03 14_[+2(2.18e-05)]_58 chrII:9282949-9283029 5.40e-02 80 chrII:6331559-6331639 1.66e-01 80 chrIII:13061262-13061342 2.40e-02 80 chrV:14685710-14685790 5.90e-05 35_[+4(1.30e-05)]_29_[+1(9.04e-05)] chrII:8185169-8185249 1.91e-01 72_[+4(7.86e-05)] chrX:6744128-6744208 2.65e-01 80 chrIII:6972067-6972147 9.81e-03 3_[+5(1.91e-05)]_69 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (5) found. ******************************************************************************** CPU: c27n05.farnam.hpc.yale.internal ********************************************************************************