******************************************************************************** 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/lsy-12.fasta CONTROL SEQUENCES= --none-- ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ chrII:1233082-1233162 1.0000 80 chrV:9860465-9860545 1.0000 80 chrV:9865228-9865308 1.0000 80 chrII:1244593-1244673 1.0000 80 chrX:12518000-12518080 1.0000 80 chrX:10691396-10691476 1.0000 80 chrI:5873989-5874069 1.0000 80 chrII:9132481-9132561 1.0000 80 chrII:1235149-1235229 1.0000 80 chrV:13090546-13090626 1.0000 80 chrIII:7369749-7369829 1.0000 80 chrI:14952724-14952804 1.0000 80 chrX:12624624-12624704 1.0000 80 chrX:17421200-17421280 1.0000 80 chrI:2672635-2672715 1.0000 80 chrIII:12017353-12017433 1.0000 80 chrIII:344456-344536 1.0000 80 chrX:12662910-12662990 1.0000 80 chrV:12543140-12543220 1.0000 80 chrX:15310431-15310511 1.0000 80 chrV:9338505-9338585 1.0000 80 chrX:15268793-15268873 1.0000 80 chrIV:8538377-8538457 1.0000 80 chrX:4143352-4143432 1.0000 80 chrX:10695043-10695123 1.0000 80 chrII:1243436-1243516 1.0000 80 chrII:548032-548112 1.0000 80 chrIV:2825608-2825688 1.0000 80 chrI:2297565-2297645 1.0000 80 chrIII:7329297-7329377 1.0000 80 chrX:10688540-10688620 1.0000 80 chrII:10553579-10553659 1.0000 80 chrI:13061193-13061273 1.0000 80 chrIII:7329498-7329578 1.0000 80 chrIII:12368493-12368573 1.0000 80 chrII:1242608-1242688 1.0000 80 chrI:7602332-7602412 1.0000 80 chrIV:11307980-11308060 1.0000 80 chrX:11486122-11486202 1.0000 80 chrV:18576427-18576507 1.0000 80 chrV:9862816-9862896 1.0000 80 chrX:15274238-15274318 1.0000 80 chrV:12548877-12548957 1.0000 80 chrII:11928870-11928950 1.0000 80 chrII:12059945-12060025 1.0000 80 chrII:554390-554470 1.0000 80 chrV:20164652-20164732 1.0000 80 chrX:15881065-15881145 1.0000 80 chrIV:3644868-3644948 1.0000 80 chrV:6220918-6220998 1.0000 80 chrII:1236648-1236728 1.0000 80 chrIV:9530796-9530876 1.0000 80 chrX:13325171-13325251 1.0000 80 chrI:6206583-6206663 1.0000 80 chrX:17626113-17626193 1.0000 80 chrX:6088831-6088911 1.0000 80 chrX:8032439-8032519 1.0000 80 chrII:4742143-4742223 1.0000 80 chrII:10450570-10450650 1.0000 80 chrI:1264968-1265048 1.0000 80 chrII:8848370-8848450 1.0000 80 chrIII:3792387-3792467 1.0000 80 chrII:4560400-4560480 1.0000 80 chrI:7857513-7857593 1.0000 80 chrV:18573322-18573402 1.0000 80 chrII:4710300-4710380 1.0000 80 chrI:3823495-3823575 1.0000 80 chrIV:7984029-7984109 1.0000 80 chrII:2378705-2378785 1.0000 80 chrV:1158359-1158439 1.0000 80 chrII:4748611-4748691 1.0000 80 chrII:551284-551364 1.0000 80 chrX:12625719-12625799 1.0000 80 chrV:13986830-13986910 1.0000 80 chrIV:16167520-16167600 1.0000 80 chrX:10690025-10690105 1.0000 80 chrI:14271472-14271552 1.0000 80 chrIII:8806638-8806718 1.0000 80 chrI:6094551-6094631 1.0000 80 chrX:10395882-10395962 1.0000 80 chrII:12055850-12055930 1.0000 80 chrII:12795398-12795478 1.0000 80 chrIII:5710852-5710932 1.0000 80 chrIV:12212341-12212421 1.0000 80 chrX:15842644-15842724 1.0000 80 chrIII:5506206-5506286 1.0000 80 chrX:15860773-15860853 1.0000 80 chrX:10647805-10647885 1.0000 80 chrX:12630780-12630860 1.0000 80 chrX:11813856-11813936 1.0000 80 chrII:15193029-15193109 1.0000 80 chrII:7319696-7319776 1.0000 80 chrI:7085981-7086061 1.0000 80 chrV:3633508-3633588 1.0000 80 chrX:10778883-10778963 1.0000 80 chrX:11410035-11410115 1.0000 80 chrII:4706520-4706600 1.0000 80 chrIII:13542827-13542907 1.0000 80 chrIII:9783164-9783244 1.0000 80 chrIV:9438875-9438955 1.0000 80 chrX:10778143-10778223 1.0000 80 chrX:10018461-10018541 1.0000 80 chrIV:13083136-13083216 1.0000 80 chrII:11926608-11926688 1.0000 80 chrIII:13719508-13719588 1.0000 80 chrII:7685010-7685090 1.0000 80 chrX:9378734-9378814 1.0000 80 chrX:2970285-2970365 1.0000 80 chrI:8302041-8302121 1.0000 80 chrI:5314696-5314776 1.0000 80 chrI:7016968-7017048 1.0000 80 chrX:10686597-10686677 1.0000 80 chrI:9333248-9333328 1.0000 80 chrII:7100845-7100925 1.0000 80 chrV:12038380-12038460 1.0000 80 chrIII:5920149-5920229 1.0000 80 chrX:15311299-15311379 1.0000 80 chrI:13060465-13060545 1.0000 80 chrI:10123412-10123492 1.0000 80 chrI:10407579-10407659 1.0000 80 chrV:5410852-5410932 1.0000 80 chrI:3826659-3826739 1.0000 80 chrIV:5805633-5805713 1.0000 80 chrII:1371725-1371805 1.0000 80 chrX:1451985-1452065 1.0000 80 chrX:10687409-10687489 1.0000 80 chrI:5372435-5372515 1.0000 80 chrIII:3902794-3902874 1.0000 80 chrI:8801880-8801960 1.0000 80 chrII:5341232-5341312 1.0000 80 chrX:15268272-15268352 1.0000 80 chrIV:2770975-2771055 1.0000 80 chrII:4719146-4719226 1.0000 80 chrII:8130898-8130978 1.0000 80 chrIII:7145557-7145637 1.0000 80 chrI:7015743-7015823 1.0000 80 chrV:8043497-8043577 1.0000 80 chrIII:10711392-10711472 1.0000 80 chrI:12041925-12042005 1.0000 80 chrIV:1867054-1867134 1.0000 80 chrIV:13893292-13893372 1.0000 80 chrX:12504138-12504218 1.0000 80 chrV:6098772-6098852 1.0000 80 chrIV:7049062-7049142 1.0000 80 chrI:9101006-9101086 1.0000 80 chrIII:5653741-5653821 1.0000 80 chrX:13164358-13164438 1.0000 80 chrX:13038963-13039043 1.0000 80 chrV:5587464-5587544 1.0000 80 chrV:9786657-9786737 1.0000 80 chrV:5838742-5838822 1.0000 80 chrV:9088965-9089045 1.0000 80 chrII:9128263-9128343 1.0000 80 chrIII:7374805-7374885 1.0000 80 chrIV:17174265-17174345 1.0000 80 chrII:4857198-4857278 1.0000 80 chrV:14008468-14008548 1.0000 80 chrX:15877156-15877236 1.0000 80 chrX:15312224-15312304 1.0000 80 chrII:4745395-4745475 1.0000 80 chrI:10777417-10777497 1.0000 80 chrII:8789075-8789155 1.0000 80 chrIII:10763181-10763261 1.0000 80 chrIV:3653491-3653571 1.0000 80 chrX:15285644-15285724 1.0000 80 chrV:14366747-14366827 1.0000 80 chrIII:13723360-13723440 1.0000 80 chrII:506186-506266 1.0000 80 chrV:11225986-11226066 1.0000 80 chrII:4575655-4575735 1.0000 80 chrI:12732955-12733035 1.0000 80 chrX:7956450-7956530 1.0000 80 chrII:6891980-6892060 1.0000 80 chrI:1273899-1273979 1.0000 80 chrV:6426154-6426234 1.0000 80 chrI:8296705-8296785 1.0000 80 chrX:10480654-10480734 1.0000 80 chrIII:4562160-4562240 1.0000 80 chrV:11802582-11802662 1.0000 80 chrII:7347526-7347606 1.0000 80 chrX:16150346-16150426 1.0000 80 chrX:15878944-15879024 1.0000 80 chrII:12878572-12878652 1.0000 80 chrX:12201736-12201816 1.0000 80 chrII:1238051-1238131 1.0000 80 chrII:2028188-2028268 1.0000 80 chrII:12058417-12058497 1.0000 80 chrIII:13779498-13779578 1.0000 80 chrX:6041000-6041080 1.0000 80 chrII:549135-549215 1.0000 80 chrV:5284763-5284843 1.0000 80 chrIII:6123751-6123831 1.0000 80 chrII:1239851-1239931 1.0000 80 chrX:8477543-8477623 1.0000 80 chrII:551484-551564 1.0000 80 chrII:11290559-11290639 1.0000 80 chrII:9211875-9211955 1.0000 80 chrX:15271632-15271712 1.0000 80 chrV:13649978-13650058 1.0000 80 chrII:8790102-8790182 1.0000 80 chrIII:7338828-7338908 1.0000 80 chrIII:3739887-3739967 1.0000 80 chrIII:11463940-11464020 1.0000 80 chrIV:2939578-2939658 1.0000 80 chrX:9952366-9952446 1.0000 80 chrII:1323287-1323367 1.0000 80 chrIV:4403746-4403826 1.0000 80 chrV:19519584-19519664 1.0000 80 chrIII:6888637-6888717 1.0000 80 chrIII:13065835-13065915 1.0000 80 chrIII:13346855-13346935 1.0000 80 chrI:9440640-9440720 1.0000 80 chrX:4146771-4146851 1.0000 80 chrIII:13724642-13724722 1.0000 80 chrV:12354606-12354686 1.0000 80 chrIII:5717669-5717749 1.0000 80 chrI:5616271-5616351 1.0000 80 chrIII:6447708-6447788 1.0000 80 chrII:4562772-4562852 1.0000 80 chrII:1148311-1148391 1.0000 80 chrIII:8979125-8979205 1.0000 80 chrIII:10534273-10534353 1.0000 80 chrI:3834421-3834501 1.0000 80 chrI:8424568-8424648 1.0000 80 chrIV:13329876-13329956 1.0000 80 chrX:11340411-11340491 1.0000 80 chrX:8017416-8017496 1.0000 80 chrIV:4026161-4026241 1.0000 80 chrIV:7397635-7397715 1.0000 80 chrI:4001234-4001314 1.0000 80 chrV:9859819-9859899 1.0000 80 chrX:1445944-1446024 1.0000 80 chrI:13650996-13651076 1.0000 80 chrX:12501024-12501104 1.0000 80 chrI:14179844-14179924 1.0000 80 chrX:11240907-11240987 1.0000 80 chrIII:10093188-10093268 1.0000 80 chrIV:10778631-10778711 1.0000 80 chrI:12045378-12045458 1.0000 80 chrX:12503492-12503572 1.0000 80 chrIII:9509984-9510064 1.0000 80 chrIII:4654023-4654103 1.0000 80 chrX:6252413-6252493 1.0000 80 chrIII:7387517-7387597 1.0000 80 chrX:6808724-6808804 1.0000 80 chrIII:6144660-6144740 1.0000 80 chrX:17545645-17545725 1.0000 80 chrIV:13388904-13388984 1.0000 80 chrIV:3370783-3370863 1.0000 80 chrIV:8529197-8529277 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_lsy-12/ -dna -nmotifs 5 -w 8 -maxsize 250000 -nostatus ../result/final_prediction/worm/fasta/RankLinear2.0_40/lsy-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= 250 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= 20000 N= 250 sample: seed= 0 hsfrac= 0 searchsize= 20000 norand= no csites= 1000 Letter frequencies in dataset: A 0.284 C 0.215 G 0.218 T 0.282 Background letter frequencies (from file dataset with add-one prior applied): A 0.284 C 0.215 G 0.218 T 0.282 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF AAAAARMG MEME-1 width = 8 sites = 37 llr = 302 E-value = 5.9e-001 ******************************************************************************** -------------------------------------------------------------------------------- Motif AAAAARMG MEME-1 Description -------------------------------------------------------------------------------- Simplified A 9aaaa531 pos.-specific C :::::15: probability G 1::::4:9 matrix T ::::::1: bits 2.2 2.0 1.8 **** 1.6 ***** * Relative 1.3 ***** * Entropy 1.1 ***** * (11.8 bits) 0.9 ***** * 0.7 ******** 0.4 ******** 0.2 ******** 0.0 -------- Multilevel AAAAAACG consensus GA sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAAAARMG MEME-1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chrIII:6144660-6144740 1 4.35e-05 . AAAAAACG AAGAAAAGGT chrIII:7387517-7387597 7 4.35e-05 ACGAAA AAAAAACG GGGGAAAAAG chrII:549135-549215 13 4.35e-05 GATTTCGATC AAAAAACG CTGAAAATGG chrII:506186-506266 4 4.35e-05 ACA AAAAAGCG CAAGGGAAGA chrI:7015743-7015823 3 4.35e-05 GA AAAAAGCG AATCGCCCAG chrII:8130898-8130978 41 4.35e-05 CCGGAAGGCG AAAAAGCG CGAAGTGCAC chrI:5314696-5314776 40 4.35e-05 AACAACAACA AAAAAACG AGAACGACCC chrI:8302041-8302121 27 4.35e-05 TTCAAGATCC AAAAAACG GGGACATCAG chrIII:8806638-8806718 65 4.35e-05 tttgttaaat aaaaaacg cgcgtgcg chrII:554390-554470 29 4.35e-05 ATTTTTCCAG AAAAAACG GACTGCACTG chrV:12548877-12548957 46 4.35e-05 CAGAGAGACG AAAAAACG ACTTTGAACT chrIII:12368493-12368573 3 4.35e-05 TG AAAAAGCG CGCGCACCCT chrIII:10093188-10093268 9 1.01e-04 CGTTCAAG AAAAAGAG TTTTTTTTCT chrX:1445944-1446024 16 1.01e-04 CCAAAGAGGG AAAAAGAG AAGAGCGAGA chrIII:6447708-6447788 48 1.01e-04 CACGAGGGAC AAAAAGAG GAGAGACTAC chrIII:4562160-4562240 13 1.01e-04 CTATCTATTG AAAAAAAG AACTAATGtt chrX:15312224-15312304 65 1.01e-04 CGAAGACCCC AAAAAGAG ACGTCTCT chrIII:7145557-7145637 55 1.01e-04 TGCCATCAAA AAAAAAAG GTTGGAATTA chrIII:3902794-3902874 27 1.01e-04 AAAGTAACCA AAAAAGAG AAAAAGTTTT chrI:13060465-13060545 39 1.01e-04 GAAAAAGGAC AAAAAAAG TGGTTGAGGG chrX:15268793-15268873 68 1.01e-04 AATAATTTTC AAAAAAAG TGTAA chrIII:344456-344536 22 1.01e-04 GAAATGGGGG AAAAAAAG GATAATGTAA chrX:12624624-12624704 37 1.01e-04 AAATCCAATG AAAAAAAG TTTATTTTTC chrI:8424568-8424648 71 1.58e-04 CCTCCTGAGG AAAAAGTG TG chrX:15311299-15311379 29 1.58e-04 TCTCTCCGGA AAAAAATG TCGGAGGTCG chrII:15193029-15193109 43 1.58e-04 GTGGCCTTGA AAAAAGTG CTGGTGGCCG chrV:13986830-13986910 11 1.58e-04 TGTACTTCCG AAAAAATG GGATTCAAAG chrV:6220918-6220998 25 1.58e-04 ccgtaggttt aaaaagtg tctgacaact chrIV:3653491-3653571 66 1.77e-04 AGTGGGTAAT AAAAACCG ACAGGGC chrI:14952724-14952804 62 1.77e-04 TAGTCTGCGG AAAAACCG GAGTTTCCTC chrII:2028188-2028268 62 2.33e-04 TTAATGGCAT AAAAAACA CTAACTTTTC chrII:7685010-7685090 2 2.33e-04 G AAAAAACA ATATTTGGTC chrIV:13083136-13083216 42 2.33e-04 TGTCGATAAT AAAAAGCA AATAACTTTT chrII:8848370-8848450 26 2.33e-04 TGCTACTCTG AAAAAGCA TGGATTGGAA chrIV:5805633-5805713 22 2.67e-04 CGAGAAGACG GAAAAACG TCGCCGCTCT chrV:1158359-1158439 46 2.67e-04 TGAAAAAGTT GAAAAGCG GCAGgctcca chrX:10686597-10686677 13 3.66e-04 GCATCACATC AAAAAAAA CCGCCTTATT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAAAARMG MEME-1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrIII:6144660-6144740 4.3e-05 [+1]_72 chrIII:7387517-7387597 4.3e-05 6_[+1]_66 chrII:549135-549215 4.3e-05 12_[+1]_60 chrII:506186-506266 4.3e-05 3_[+1]_69 chrI:7015743-7015823 4.3e-05 2_[+1]_70 chrII:8130898-8130978 4.3e-05 40_[+1]_32 chrI:5314696-5314776 4.3e-05 39_[+1]_33 chrI:8302041-8302121 4.3e-05 26_[+1]_46 chrIII:8806638-8806718 4.3e-05 64_[+1]_8 chrII:554390-554470 4.3e-05 28_[+1]_44 chrV:12548877-12548957 4.3e-05 45_[+1]_27 chrIII:12368493-12368573 4.3e-05 2_[+1]_70 chrIII:10093188-10093268 0.0001 8_[+1]_64 chrX:1445944-1446024 0.0001 15_[+1]_57 chrIII:6447708-6447788 0.0001 47_[+1]_25 chrIII:4562160-4562240 0.0001 12_[+1]_60 chrX:15312224-15312304 0.0001 64_[+1]_8 chrIII:7145557-7145637 0.0001 54_[+1]_18 chrIII:3902794-3902874 0.0001 26_[+1]_46 chrI:13060465-13060545 0.0001 38_[+1]_34 chrX:15268793-15268873 0.0001 67_[+1]_5 chrIII:344456-344536 0.0001 21_[+1]_51 chrX:12624624-12624704 0.0001 36_[+1]_36 chrI:8424568-8424648 0.00016 70_[+1]_2 chrX:15311299-15311379 0.00016 28_[+1]_44 chrII:15193029-15193109 0.00016 42_[+1]_30 chrV:13986830-13986910 0.00016 10_[+1]_62 chrV:6220918-6220998 0.00016 24_[+1]_48 chrIV:3653491-3653571 0.00018 65_[+1]_7 chrI:14952724-14952804 0.00018 61_[+1]_11 chrII:2028188-2028268 0.00023 61_[+1]_11 chrII:7685010-7685090 0.00023 1_[+1]_71 chrIV:13083136-13083216 0.00023 41_[+1]_31 chrII:8848370-8848450 0.00023 25_[+1]_47 chrIV:5805633-5805713 0.00027 21_[+1]_51 chrV:1158359-1158439 0.00027 45_[+1]_27 chrX:10686597-10686677 0.00037 12_[+1]_60 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAAAARMG MEME-1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF AAAAARMG width=8 seqs=37 chrIII:6144660-6144740 ( 1) AAAAAACG 1 chrIII:7387517-7387597 ( 7) AAAAAACG 1 chrII:549135-549215 ( 13) AAAAAACG 1 chrII:506186-506266 ( 4) AAAAAGCG 1 chrI:7015743-7015823 ( 3) AAAAAGCG 1 chrII:8130898-8130978 ( 41) AAAAAGCG 1 chrI:5314696-5314776 ( 40) AAAAAACG 1 chrI:8302041-8302121 ( 27) AAAAAACG 1 chrIII:8806638-8806718 ( 65) AAAAAACG 1 chrII:554390-554470 ( 29) AAAAAACG 1 chrV:12548877-12548957 ( 46) AAAAAACG 1 chrIII:12368493-12368573 ( 3) AAAAAGCG 1 chrIII:10093188-10093268 ( 9) AAAAAGAG 1 chrX:1445944-1446024 ( 16) AAAAAGAG 1 chrIII:6447708-6447788 ( 48) AAAAAGAG 1 chrIII:4562160-4562240 ( 13) AAAAAAAG 1 chrX:15312224-15312304 ( 65) AAAAAGAG 1 chrIII:7145557-7145637 ( 55) AAAAAAAG 1 chrIII:3902794-3902874 ( 27) AAAAAGAG 1 chrI:13060465-13060545 ( 39) AAAAAAAG 1 chrX:15268793-15268873 ( 68) AAAAAAAG 1 chrIII:344456-344536 ( 22) AAAAAAAG 1 chrX:12624624-12624704 ( 37) AAAAAAAG 1 chrI:8424568-8424648 ( 71) AAAAAGTG 1 chrX:15311299-15311379 ( 29) AAAAAATG 1 chrII:15193029-15193109 ( 43) AAAAAGTG 1 chrV:13986830-13986910 ( 11) AAAAAATG 1 chrV:6220918-6220998 ( 25) AAAAAGTG 1 chrIV:3653491-3653571 ( 66) AAAAACCG 1 chrI:14952724-14952804 ( 62) AAAAACCG 1 chrII:2028188-2028268 ( 62) AAAAAACA 1 chrII:7685010-7685090 ( 2) AAAAAACA 1 chrIV:13083136-13083216 ( 42) AAAAAGCA 1 chrII:8848370-8848450 ( 26) AAAAAGCA 1 chrIV:5805633-5805713 ( 22) GAAAAACG 1 chrV:1158359-1158439 ( 46) GAAAAGCG 1 chrX:10686597-10686677 ( 13) AAAAAAAA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAAAARMG MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 18250 bayes= 10.3679 E= 5.9e-001 174 -1185 -201 -1185 182 -1185 -1185 -1185 182 -1185 -1185 -1185 182 -1185 -1185 -1185 182 -1185 -1185 -1185 93 -199 89 -1185 19 133 -1185 -106 -107 -1185 199 -1185 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAAAARMG MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 37 E= 5.9e-001 0.945946 0.000000 0.054054 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 0.000000 0.540541 0.054054 0.405405 0.000000 0.324324 0.540541 0.000000 0.135135 0.135135 0.000000 0.864865 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAAAARMG MEME-1 regular expression -------------------------------------------------------------------------------- AAAAA[AG][CA]G -------------------------------------------------------------------------------- Time 5.87 secs. ******************************************************************************** ******************************************************************************** MOTIF MMWTTTTY MEME-2 width = 8 sites = 81 llr = 545 E-value = 3.2e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif MMWTTTTY MEME-2 Description -------------------------------------------------------------------------------- Simplified A 545::::: pos.-specific C 432::::7 probability G :2:::::: matrix T 113aaaa3 bits 2.2 2.0 1.8 **** 1.6 **** Relative 1.3 **** Entropy 1.1 ***** (9.7 bits) 0.9 ***** 0.7 * ***** 0.4 * ****** 0.2 ******** 0.0 -------- Multilevel AAATTTTC consensus CCT T sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif MMWTTTTY MEME-2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chrX:4146771-4146851 53 4.14e-05 GAACCTCCAA CCATTTTC GCAAGCACAA chrI:12041925-12042005 45 4.14e-05 TCCAAGATTT CAATTTTC CCATCAAATC chrI:6094551-6094631 7 4.14e-05 catgat caattttc ttaaatttga chrIII:3792387-3792467 66 4.14e-05 CTGAGCTCTT CAATTTTC TCATCTT chrIII:9509984-9510064 40 9.62e-05 GTTCGGCAGA ACATTTTC CTTGCCTATT chrII:1148311-1148391 29 9.62e-05 ACCAAAAATC AAATTTTC TTTCAGCAAT chrIII:7374805-7374885 71 9.62e-05 CCATATTGCC AAATTTTC AG chrI:3823495-3823575 37 9.62e-05 TCAATTTTTG AAATTTTC ATCTGTCGCA chrX:6088831-6088911 33 9.62e-05 GATTGTGGCG ACATTTTC AATTTATGCA chrI:6206583-6206663 20 9.62e-05 TGAAACCAAT ACATTTTC TCAGTCTGAA chrII:554390-554470 5 9.62e-05 CCCC AAATTTTC CCAAATATTT chrV:18576427-18576507 12 9.62e-05 GGATTTTTTG AAATTTTC GGAAAAAAAT chrX:15310431-15310511 26 9.62e-05 CCAGTGCGCT ACATTTTC ATCCGATGCT chrV:12543140-12543220 52 9.62e-05 GCAGAATGTC ACATTTTC AGAGAATGAC chrIII:12017353-12017433 61 9.62e-05 agttttcgac aaattttc cgtttaccgg chrIII:7369749-7369829 17 9.62e-05 CATTGTTTCA AAATTTTC TTGGATTTTA chrIV:8529197-8529277 48 1.37e-04 TTCGTCTTCG CCTTTTTC AGTGACGACG chrI:10123412-10123492 19 1.37e-04 TTGTGGCTGA CCTTTTTC GGTGAACGAG chrV:5838742-5838822 52 1.92e-04 TTTTGGCTGT AATTTTTC GAAAACGAAC chrX:10687409-10687489 52 1.92e-04 CGTTATGTTA ACTTTTTC AGAATGAAGC chrI:3826659-3826739 37 1.92e-04 GAagatgcga aatttttc gattttcgtg chrI:13060465-13060545 12 1.92e-04 CGCGTGAATC ACTTTTTC GAAACGGAAG chrIII:5506206-5506286 48 1.92e-04 CGTCTACTCT AATTTTTC CCCTTTCCTA chrX:12624624-12624704 3 1.92e-04 TT ACTTTTTC AAACAAAAAT chrI:10777417-10777497 31 2.41e-04 AGACTCCGCC CACTTTTC GCTTGACGAA chrV:14008468-14008548 68 2.41e-04 ATCTATCTCT CACTTTTC ACATA chrX:9378734-9378814 60 2.41e-04 TCATCTGCTA CCCTTTTC AAGCCCCGCC chrII:7319696-7319776 4 2.41e-04 GTT CCCTTTTC TCCCATGCGC chrX:12630780-12630860 43 2.41e-04 TCGGGGGTTA CCCTTTTC ATCTTCAGAC chrIII:7329498-7329578 52 2.41e-04 GTCTCTCCTT CGATTTTC AGATTATCTA chrX:9952366-9952446 54 3.06e-04 ATCTGCACTG ACCTTTTC ATGAGACATC chrII:5341232-5341312 42 3.06e-04 ATTTTAAATC AGATTTTC GGGAACATCC chrII:12055850-12055930 42 3.06e-04 TAAATCCAAA AACTTTTC CAGAAACGCC chrV:9338505-9338585 42 3.06e-04 GAATAATTTT AGATTTTC AGGGCAAGGA chrX:12501024-12501104 1 3.61e-04 . CAATTTTT CGAGTTGTTA chrI:13650996-13651076 66 3.61e-04 TGGAGGAAAA CAATTTTT TTTGGGA chrX:6041000-6041080 73 3.61e-04 TGTATTCAAT CAATTTTT chrV:9786657-9786737 49 3.61e-04 GTCTGAACTG CAATTTTT TCACATTTCT chrIV:9438875-9438955 31 3.61e-04 TAAAATTCTT CAATTTTT GTATGATTTA chrIII:8806638-8806718 50 3.61e-04 ctcgacacga caattttt gttaaataaa chrIII:13346855-13346935 9 4.33e-04 CTAAAAAA AAATTTTT TTCTGAAAAA chrX:15271632-15271712 64 4.33e-04 tgctgacgtc acattttt tgggcaaaa chrII:2028188-2028268 43 4.33e-04 GAAAATCGAT AAATTTTT TTTAATGGCA chrI:8801880-8801960 10 4.33e-04 ATATCTACA ACATTTTT TGCATTTGCT chrIV:4026161-4026241 9 4.51e-04 CCGTTTTT CGTTTTTC AGCTGTTCCG chrX:15860773-15860853 12 4.51e-04 TTATTCTTGG CGTTTTTC ACGTCCGGAG chrX:15274238-15274318 45 4.51e-04 TGTTTTCAGG CGTTTTTC TGTCACCTCG chrX:2970285-2970365 46 4.74e-04 CAAGGACAAG AGTTTTTC TTTTTTTTTA chrIV:12212341-12212421 53 4.74e-04 ACGATTCGGC AGTTTTTC TCTGAAAATT chrIII:8979125-8979205 19 5.28e-04 ATCTTTCTCT CATTTTTT CATTGATTAT chrV:12038380-12038460 65 5.28e-04 GTCGTCTTTC CCTTTTTT CTTGTCGC chrIV:13083136-13083216 13 5.28e-04 TTATCTTGCG CCTTTTTT CGAAAGTTGT chrI:14271472-14271552 8 5.28e-04 attcccg catttttt gtagatcaaa chrX:8032439-8032519 51 5.28e-04 GCATATATGA CCTTTTTT GCCCAGTGGA chrI:12045378-12045458 31 6.13e-04 GGAAAATTTG AATTTTTT TCCCGTTTTT chrIV:16167520-16167600 59 6.13e-04 CTTCCATGTT AATTTTTT CATCATGTTT chrII:1233082-1233162 17 6.13e-04 TAACGACTGT ACTTTTTT TCTTGAGAAA chrIII:6144660-6144740 37 6.86e-04 AAGTTGATTA TAATTTTC CAAATCGCAA chrII:11290559-11290639 25 6.86e-04 ATCCCAAACC TCATTTTC AGCGCGAAAT chrV:11225986-11226066 7 6.86e-04 ATATAC AGCTTTTC CATAATTCCA chrIV:7984029-7984109 15 6.86e-04 ACAGAATGTG AGCTTTTC TTGCCTTGGC chrX:15268793-15268873 60 6.86e-04 TATTAATCAA TAATTTTC AAAAAAAGTG chrX:15878944-15879024 29 7.50e-04 TACTATACGT CACTTTTT GCCCTCTTTC chrI:12732955-12733035 41 7.50e-04 CGAGAAAATT CGATTTTT TTAAAAAGTT chrII:4857198-4857278 47 7.50e-04 CTGTTTCAAA CGATTTTT CTCTCATCGT chrX:10688540-10688620 9 7.50e-04 CTCGTTTA CCCTTTTT AAAGGTCTTG chrI:8424568-8424648 46 8.60e-04 TATTGGAGAA AACTTTTT ATGGTCGCCT chrIV:2939578-2939658 28 8.60e-04 TGCCGCATGC CTATTTTC TAACTATATG chrIV:7049062-7049142 46 8.60e-04 TATAGATCGT CTATTTTC CATCTCCCCA chrI:1264968-1265048 19 8.60e-04 GCCGAGTTTG CTATTTTC TGCGGCCACG chrIV:4403746-4403826 12 8.91e-04 GGTCATCATC ATATTTTC GTGACATTCT chrII:4560400-4560480 24 9.44e-04 ACTACTCTAC TCTTTTTC TACTTGCCAG chrII:12059945-12060025 28 9.44e-04 AGGCACATGG TATTTTTC AGAGTGGGTC chrIII:3902794-3902874 39 1.02e-03 AAAGAGAAAA AGTTTTTT GGGGAGCGCA chrII:15193029-15193109 61 1.02e-03 CTGGTGGCCG AGTTTTTT TTAATGACCA chrII:8789075-8789155 39 1.12e-03 CCGATGTCTA TACTTTTC GTAATAAAAG chrX:10395882-10395962 10 1.12e-03 CATGCACTG TCCTTTTC TACACCATTC chrII:9132481-9132561 11 1.12e-03 TCCACTGGAA TACTTTTC TGGCATTCGG chrX:11240907-11240987 17 1.25e-03 ATGTATGATG TCATTTTT GGGAACAAGA chrV:8043497-8043577 67 1.33e-03 TATCGTCTCT CTATTTTT GACCAC chrV:13090546-13090626 71 1.37e-03 ttttcttcaa atattttt ta -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif MMWTTTTY MEME-2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrX:4146771-4146851 4.1e-05 52_[+2]_20 chrI:12041925-12042005 4.1e-05 44_[+2]_28 chrI:6094551-6094631 4.1e-05 6_[+2]_66 chrIII:3792387-3792467 4.1e-05 65_[+2]_7 chrIII:9509984-9510064 9.6e-05 39_[+2]_33 chrII:1148311-1148391 9.6e-05 28_[+2]_44 chrIII:7374805-7374885 9.6e-05 70_[+2]_2 chrI:3823495-3823575 9.6e-05 36_[+2]_36 chrX:6088831-6088911 9.6e-05 32_[+2]_40 chrI:6206583-6206663 9.6e-05 19_[+2]_53 chrII:554390-554470 9.6e-05 4_[+2]_68 chrV:18576427-18576507 9.6e-05 11_[+2]_61 chrX:15310431-15310511 9.6e-05 25_[+2]_47 chrV:12543140-12543220 9.6e-05 51_[+2]_21 chrIII:12017353-12017433 9.6e-05 60_[+2]_12 chrIII:7369749-7369829 9.6e-05 16_[+2]_56 chrIV:8529197-8529277 0.00014 47_[+2]_25 chrI:10123412-10123492 0.00014 18_[+2]_54 chrV:5838742-5838822 0.00019 51_[+2]_21 chrX:10687409-10687489 0.00019 51_[+2]_21 chrI:3826659-3826739 0.00019 36_[+2]_36 chrI:13060465-13060545 0.00019 11_[+2]_61 chrIII:5506206-5506286 0.00019 47_[+2]_25 chrX:12624624-12624704 0.00019 2_[+2]_70 chrI:10777417-10777497 0.00024 30_[+2]_42 chrV:14008468-14008548 0.00024 67_[+2]_5 chrX:9378734-9378814 0.00024 59_[+2]_13 chrII:7319696-7319776 0.00024 3_[+2]_69 chrX:12630780-12630860 0.00024 42_[+2]_30 chrIII:7329498-7329578 0.00024 51_[+2]_21 chrX:9952366-9952446 0.00031 53_[+2]_19 chrII:5341232-5341312 0.00031 41_[+2]_31 chrII:12055850-12055930 0.00031 41_[+2]_31 chrV:9338505-9338585 0.00031 41_[+2]_31 chrX:12501024-12501104 0.00036 [+2]_72 chrI:13650996-13651076 0.00036 65_[+2]_7 chrX:6041000-6041080 0.00036 72_[+2] chrV:9786657-9786737 0.00036 48_[+2]_24 chrIV:9438875-9438955 0.00036 30_[+2]_42 chrIII:8806638-8806718 0.00036 49_[+2]_23 chrIII:13346855-13346935 0.00043 8_[+2]_64 chrX:15271632-15271712 0.00043 63_[+2]_9 chrII:2028188-2028268 0.00043 42_[+2]_30 chrI:8801880-8801960 0.00043 9_[+2]_63 chrIV:4026161-4026241 0.00045 8_[+2]_64 chrX:15860773-15860853 0.00045 11_[+2]_61 chrX:15274238-15274318 0.00045 44_[+2]_28 chrX:2970285-2970365 0.00047 45_[+2]_27 chrIV:12212341-12212421 0.00047 52_[+2]_20 chrIII:8979125-8979205 0.00053 18_[+2]_54 chrV:12038380-12038460 0.00053 64_[+2]_8 chrIV:13083136-13083216 0.00053 12_[+2]_60 chrI:14271472-14271552 0.00053 7_[+2]_65 chrX:8032439-8032519 0.00053 50_[+2]_22 chrI:12045378-12045458 0.00061 30_[+2]_42 chrIV:16167520-16167600 0.00061 58_[+2]_14 chrII:1233082-1233162 0.00061 16_[+2]_56 chrIII:6144660-6144740 0.00069 36_[+2]_36 chrII:11290559-11290639 0.00069 24_[+2]_48 chrV:11225986-11226066 0.00069 6_[+2]_66 chrIV:7984029-7984109 0.00069 14_[+2]_58 chrX:15268793-15268873 0.00069 59_[+2]_13 chrX:15878944-15879024 0.00075 28_[+2]_44 chrI:12732955-12733035 0.00075 40_[+2]_32 chrII:4857198-4857278 0.00075 46_[+2]_26 chrX:10688540-10688620 0.00075 8_[+2]_64 chrI:8424568-8424648 0.00086 45_[+2]_27 chrIV:2939578-2939658 0.00086 27_[+2]_45 chrIV:7049062-7049142 0.00086 45_[+2]_27 chrI:1264968-1265048 0.00086 18_[+2]_54 chrIV:4403746-4403826 0.00089 11_[+2]_61 chrII:4560400-4560480 0.00094 23_[+2]_49 chrII:12059945-12060025 0.00094 27_[+2]_45 chrIII:3902794-3902874 0.001 38_[+2]_34 chrII:15193029-15193109 0.001 60_[+2]_12 chrII:8789075-8789155 0.0011 38_[+2]_34 chrX:10395882-10395962 0.0011 9_[+2]_63 chrII:9132481-9132561 0.0011 10_[+2]_62 chrX:11240907-11240987 0.0012 16_[+2]_56 chrV:8043497-8043577 0.0013 66_[+2]_6 chrV:13090546-13090626 0.0014 70_[+2]_2 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif MMWTTTTY MEME-2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF MMWTTTTY width=8 seqs=81 chrX:4146771-4146851 ( 53) CCATTTTC 1 chrI:12041925-12042005 ( 45) CAATTTTC 1 chrI:6094551-6094631 ( 7) CAATTTTC 1 chrIII:3792387-3792467 ( 66) CAATTTTC 1 chrIII:9509984-9510064 ( 40) ACATTTTC 1 chrII:1148311-1148391 ( 29) AAATTTTC 1 chrIII:7374805-7374885 ( 71) AAATTTTC 1 chrI:3823495-3823575 ( 37) AAATTTTC 1 chrX:6088831-6088911 ( 33) ACATTTTC 1 chrI:6206583-6206663 ( 20) ACATTTTC 1 chrII:554390-554470 ( 5) AAATTTTC 1 chrV:18576427-18576507 ( 12) AAATTTTC 1 chrX:15310431-15310511 ( 26) ACATTTTC 1 chrV:12543140-12543220 ( 52) ACATTTTC 1 chrIII:12017353-12017433 ( 61) AAATTTTC 1 chrIII:7369749-7369829 ( 17) AAATTTTC 1 chrIV:8529197-8529277 ( 48) CCTTTTTC 1 chrI:10123412-10123492 ( 19) CCTTTTTC 1 chrV:5838742-5838822 ( 52) AATTTTTC 1 chrX:10687409-10687489 ( 52) ACTTTTTC 1 chrI:3826659-3826739 ( 37) AATTTTTC 1 chrI:13060465-13060545 ( 12) ACTTTTTC 1 chrIII:5506206-5506286 ( 48) AATTTTTC 1 chrX:12624624-12624704 ( 3) ACTTTTTC 1 chrI:10777417-10777497 ( 31) CACTTTTC 1 chrV:14008468-14008548 ( 68) CACTTTTC 1 chrX:9378734-9378814 ( 60) CCCTTTTC 1 chrII:7319696-7319776 ( 4) CCCTTTTC 1 chrX:12630780-12630860 ( 43) CCCTTTTC 1 chrIII:7329498-7329578 ( 52) CGATTTTC 1 chrX:9952366-9952446 ( 54) ACCTTTTC 1 chrII:5341232-5341312 ( 42) AGATTTTC 1 chrII:12055850-12055930 ( 42) AACTTTTC 1 chrV:9338505-9338585 ( 42) AGATTTTC 1 chrX:12501024-12501104 ( 1) CAATTTTT 1 chrI:13650996-13651076 ( 66) CAATTTTT 1 chrX:6041000-6041080 ( 73) CAATTTTT 1 chrV:9786657-9786737 ( 49) CAATTTTT 1 chrIV:9438875-9438955 ( 31) CAATTTTT 1 chrIII:8806638-8806718 ( 50) CAATTTTT 1 chrIII:13346855-13346935 ( 9) AAATTTTT 1 chrX:15271632-15271712 ( 64) ACATTTTT 1 chrII:2028188-2028268 ( 43) AAATTTTT 1 chrI:8801880-8801960 ( 10) ACATTTTT 1 chrIV:4026161-4026241 ( 9) CGTTTTTC 1 chrX:15860773-15860853 ( 12) CGTTTTTC 1 chrX:15274238-15274318 ( 45) CGTTTTTC 1 chrX:2970285-2970365 ( 46) AGTTTTTC 1 chrIV:12212341-12212421 ( 53) AGTTTTTC 1 chrIII:8979125-8979205 ( 19) CATTTTTT 1 chrV:12038380-12038460 ( 65) CCTTTTTT 1 chrIV:13083136-13083216 ( 13) CCTTTTTT 1 chrI:14271472-14271552 ( 8) CATTTTTT 1 chrX:8032439-8032519 ( 51) CCTTTTTT 1 chrI:12045378-12045458 ( 31) AATTTTTT 1 chrIV:16167520-16167600 ( 59) AATTTTTT 1 chrII:1233082-1233162 ( 17) ACTTTTTT 1 chrIII:6144660-6144740 ( 37) TAATTTTC 1 chrII:11290559-11290639 ( 25) TCATTTTC 1 chrV:11225986-11226066 ( 7) AGCTTTTC 1 chrIV:7984029-7984109 ( 15) AGCTTTTC 1 chrX:15268793-15268873 ( 60) TAATTTTC 1 chrX:15878944-15879024 ( 29) CACTTTTT 1 chrI:12732955-12733035 ( 41) CGATTTTT 1 chrII:4857198-4857278 ( 47) CGATTTTT 1 chrX:10688540-10688620 ( 9) CCCTTTTT 1 chrI:8424568-8424648 ( 46) AACTTTTT 1 chrIV:2939578-2939658 ( 28) CTATTTTC 1 chrIV:7049062-7049142 ( 46) CTATTTTC 1 chrI:1264968-1265048 ( 19) CTATTTTC 1 chrIV:4403746-4403826 ( 12) ATATTTTC 1 chrII:4560400-4560480 ( 24) TCTTTTTC 1 chrII:12059945-12060025 ( 28) TATTTTTC 1 chrIII:3902794-3902874 ( 39) AGTTTTTT 1 chrII:15193029-15193109 ( 61) AGTTTTTT 1 chrII:8789075-8789155 ( 39) TACTTTTC 1 chrX:10395882-10395962 ( 10) TCCTTTTC 1 chrII:9132481-9132561 ( 11) TACTTTTC 1 chrX:11240907-11240987 ( 17) TCATTTTT 1 chrV:8043497-8043577 ( 67) CTATTTTT 1 chrV:13090546-13090626 ( 71) ATATTTTT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif MMWTTTTY MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 18250 bayes= 9.65557 E= 3.2e+001 72 96 -1298 -135 61 58 -34 -193 83 -22 -1298 13 -1298 -1298 -1298 182 -1298 -1298 -1298 182 -1298 -1298 -1298 182 -1298 -1298 -1298 182 -1298 160 -1298 29 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif MMWTTTTY MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 81 E= 3.2e+001 0.469136 0.419753 0.000000 0.111111 0.432099 0.320988 0.172840 0.074074 0.506173 0.185185 0.000000 0.308642 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 0.000000 1.000000 0.000000 0.654321 0.000000 0.345679 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif MMWTTTTY MEME-2 regular expression -------------------------------------------------------------------------------- [AC][AC][AT]TTTT[CT] -------------------------------------------------------------------------------- Time 9.56 secs. ******************************************************************************** ******************************************************************************** MOTIF CCRCCGCC MEME-3 width = 8 sites = 2 llr = 23 E-value = 9.9e+004 ******************************************************************************** -------------------------------------------------------------------------------- Motif CCRCCGCC MEME-3 Description -------------------------------------------------------------------------------- Simplified A ::5::::: pos.-specific C aa:aa:aa probability G ::5::a:: matrix T :::::::: bits 2.2 ** ***** 2.0 ** ***** 1.8 ** ***** 1.6 ** ***** Relative 1.3 ** ***** Entropy 1.1 ******** (16.5 bits) 0.9 ******** 0.7 ******** 0.4 ******** 0.2 ******** 0.0 -------- Multilevel CCACCGCC consensus G sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCRCCGCC MEME-3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chrV:14366747-14366827 60 4.69e-06 TCTCTCCGTG CCGCCGCC TCGCTCTCCG chrX:10395882-10395962 30 1.08e-05 CACCATTCTT CCACCGCC GTTGTGTGTT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCRCCGCC MEME-3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrV:14366747-14366827 4.7e-06 59_[+3]_13 chrX:10395882-10395962 1.1e-05 29_[+3]_43 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCRCCGCC MEME-3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF CCRCCGCC width=8 seqs=2 chrV:14366747-14366827 ( 60) CCGCCGCC 1 chrX:10395882-10395962 ( 30) CCACCGCC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCRCCGCC MEME-3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 18250 bayes= 12.3073 E= 9.9e+004 -765 221 -765 -765 -765 221 -765 -765 81 -765 119 -765 -765 221 -765 -765 -765 221 -765 -765 -765 -765 219 -765 -765 221 -765 -765 -765 221 -765 -765 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCRCCGCC MEME-3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 2 E= 9.9e+004 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.500000 0.000000 0.500000 0.000000 0.000000 1.000000 0.000000 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 0.000000 1.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCRCCGCC MEME-3 regular expression -------------------------------------------------------------------------------- CC[AG]CCGCC -------------------------------------------------------------------------------- Time 13.10 secs. ******************************************************************************** ******************************************************************************** MOTIF ACACCACG MEME-4 width = 8 sites = 5 llr = 57 E-value = 1.3e+004 ******************************************************************************** -------------------------------------------------------------------------------- Motif ACACCACG MEME-4 Description -------------------------------------------------------------------------------- Simplified A a:a::a:: pos.-specific C :a:aa:a: probability G :::::::a matrix T :::::::: bits 2.2 * ** ** 2.0 * ** ** 1.8 ******** 1.6 ******** Relative 1.3 ******** Entropy 1.1 ******** (16.5 bits) 0.9 ******** 0.7 ******** 0.4 ******** 0.2 ******** 0.0 -------- Multilevel ACACCACG consensus sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ACACCACG MEME-4 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chrIII:13724642-13724722 39 1.07e-05 ggacacactg acaccacg tTGTGGTTTC chrIII:6888637-6888717 32 1.07e-05 GCTGACCATT ACACCACG AACGCGGCAT chrX:13164358-13164438 52 1.07e-05 ATGAGGATAC ACACCACG CATAGTTATT chrI:14271472-14271552 44 1.07e-05 gggcattctg acaccacg tgTTTATAGG chrV:13090546-13090626 42 1.07e-05 tgtagtctca acaccacg tttacttact -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ACACCACG MEME-4 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrIII:13724642-13724722 1.1e-05 38_[+4]_34 chrIII:6888637-6888717 1.1e-05 31_[+4]_41 chrX:13164358-13164438 1.1e-05 51_[+4]_21 chrI:14271472-14271552 1.1e-05 43_[+4]_29 chrV:13090546-13090626 1.1e-05 41_[+4]_31 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ACACCACG MEME-4 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF ACACCACG width=8 seqs=5 chrIII:13724642-13724722 ( 39) ACACCACG 1 chrIII:6888637-6888717 ( 32) ACACCACG 1 chrX:13164358-13164438 ( 52) ACACCACG 1 chrI:14271472-14271552 ( 44) ACACCACG 1 chrV:13090546-13090626 ( 42) ACACCACG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ACACCACG MEME-4 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 18250 bayes= 11.2675 E= 1.3e+004 181 -897 -897 -897 -897 221 -897 -897 181 -897 -897 -897 -897 221 -897 -897 -897 221 -897 -897 181 -897 -897 -897 -897 221 -897 -897 -897 -897 219 -897 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ACACCACG MEME-4 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 5 E= 1.3e+004 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ACACCACG MEME-4 regular expression -------------------------------------------------------------------------------- ACACCACG -------------------------------------------------------------------------------- Time 16.65 secs. ******************************************************************************** ******************************************************************************** MOTIF SCGCGCGC MEME-5 width = 8 sites = 2 llr = 23 E-value = 1.3e+005 ******************************************************************************** -------------------------------------------------------------------------------- Motif SCGCGCGC MEME-5 Description -------------------------------------------------------------------------------- Simplified A :::::::: pos.-specific C 5a:a:a:a probability G 5:a:a:a: matrix T :::::::: bits 2.2 ******* 2.0 ******* 1.8 ******* 1.6 ******* Relative 1.3 ******* Entropy 1.1 ******** (16.7 bits) 0.9 ******** 0.7 ******** 0.4 ******** 0.2 ******** 0.0 -------- Multilevel CCGCGCGC consensus G sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif SCGCGCGC MEME-5 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chrIII:12368493-12368573 57 9.59e-06 CGGTCGAAAT GCGCGCGC TTAGTAGGTG chrII:1244593-1244673 7 9.59e-06 ccgctc ccgcgcgc cgcgcAATCG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif SCGCGCGC MEME-5 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrIII:12368493-12368573 9.6e-06 56_[+5]_16 chrII:1244593-1244673 9.6e-06 6_[+5]_66 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif SCGCGCGC MEME-5 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF SCGCGCGC width=8 seqs=2 chrIII:12368493-12368573 ( 57) GCGCGCGC 1 chrII:1244593-1244673 ( 7) CCGCGCGC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif SCGCGCGC MEME-5 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 18250 bayes= 12.3073 E= 1.3e+005 -765 121 119 -765 -765 221 -765 -765 -765 -765 219 -765 -765 221 -765 -765 -765 -765 219 -765 -765 221 -765 -765 -765 -765 219 -765 -765 221 -765 -765 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif SCGCGCGC MEME-5 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 2 E= 1.3e+005 0.000000 0.500000 0.500000 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 0.000000 0.000000 1.000000 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 SCGCGCGC MEME-5 regular expression -------------------------------------------------------------------------------- [CG]CGCGCGC -------------------------------------------------------------------------------- Time 20.23 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrII:1233082-1233162 1.24e-01 80 chrV:9860465-9860545 9.18e-01 80 chrV:9865228-9865308 7.56e-01 80 chrII:1244593-1244673 8.58e-03 6_[+5(9.59e-06)]_66 chrX:12518000-12518080 3.69e-01 80 chrX:10691396-10691476 8.48e-01 80 chrI:5873989-5874069 4.41e-01 80 chrII:9132481-9132561 7.29e-01 80 chrII:1235149-1235229 6.14e-01 80 chrV:13090546-13090626 2.58e-03 41_[+4(1.07e-05)]_31 chrIII:7369749-7369829 3.65e-01 16_[+2(9.62e-05)]_56 chrI:14952724-14952804 2.34e-01 80 chrX:12624624-12624704 4.59e-02 80 chrX:17421200-17421280 9.51e-01 80 chrI:2672635-2672715 9.09e-01 80 chrIII:12017353-12017433 3.85e-01 [+2(9.62e-05)]_52_[+2(9.62e-05)]_12 chrIII:344456-344536 2.08e-01 80 chrX:12662910-12662990 3.78e-01 80 chrV:12543140-12543220 1.20e-01 51_[+2(9.62e-05)]_21 chrX:15310431-15310511 1.14e-02 25_[+2(9.62e-05)]_47 chrV:9338505-9338585 5.90e-01 80 chrX:15268793-15268873 1.17e-02 80 chrIV:8538377-8538457 8.20e-01 80 chrX:4143352-4143432 6.37e-01 80 chrX:10695043-10695123 7.46e-01 80 chrII:1243436-1243516 9.71e-01 80 chrII:548032-548112 2.51e-01 80 chrIV:2825608-2825688 9.74e-01 80 chrI:2297565-2297645 5.09e-02 48_[+5(9.59e-06)]_24 chrIII:7329297-7329377 9.81e-01 80 chrX:10688540-10688620 4.36e-01 80 chrII:10553579-10553659 9.94e-01 80 chrI:13061193-13061273 9.24e-01 80 chrIII:7329498-7329578 5.23e-01 80 chrIII:12368493-12368573 9.19e-06 7_[+5(9.59e-06)]_41_[+5(9.59e-06)]_\ 16 chrII:1242608-1242688 5.12e-01 80 chrI:7602332-7602412 8.67e-01 80 chrIV:11307980-11308060 8.64e-01 80 chrX:11486122-11486202 9.33e-01 80 chrV:18576427-18576507 5.25e-02 11_[+2(9.62e-05)]_61 chrV:9862816-9862896 3.48e-01 80 chrX:15274238-15274318 2.75e-03 80 chrV:12548877-12548957 2.67e-03 45_[+1(4.35e-05)]_27 chrII:11928870-11928950 6.21e-01 80 chrII:12059945-12060025 1.10e-01 80 chrII:554390-554470 1.48e-02 4_[+2(9.62e-05)]_16_[+1(4.35e-05)]_\ 44 chrV:20164652-20164732 1.76e-01 80 chrX:15881065-15881145 9.01e-01 80 chrIV:3644868-3644948 6.83e-01 80 chrV:6220918-6220998 1.81e-01 80 chrII:1236648-1236728 4.59e-01 80 chrIV:9530796-9530876 8.34e-01 80 chrX:13325171-13325251 4.81e-01 80 chrI:6206583-6206663 3.24e-01 19_[+2(9.62e-05)]_53 chrX:17626113-17626193 9.42e-01 80 chrX:6088831-6088911 4.05e-01 32_[+2(9.62e-05)]_40 chrX:8032439-8032519 4.29e-01 80 chrII:4742143-4742223 7.96e-01 80 chrII:10450570-10450650 1.47e-01 80 chrI:1264968-1265048 5.19e-02 80 chrII:8848370-8848450 4.03e-01 80 chrIII:3792387-3792467 8.53e-02 65_[+2(4.14e-05)]_7 chrII:4560400-4560480 5.37e-01 80 chrI:7857513-7857593 7.46e-01 80 chrV:18573322-18573402 1.25e-01 80 chrII:4710300-4710380 7.57e-01 80 chrI:3823495-3823575 1.58e-01 36_[+2(9.62e-05)]_36 chrIV:7984029-7984109 4.30e-01 80 chrII:2378705-2378785 5.03e-01 80 chrV:1158359-1158439 5.72e-02 80 chrII:4748611-4748691 4.58e-01 80 chrII:551284-551364 1.42e-01 80 chrX:12625719-12625799 1.44e-01 80 chrV:13986830-13986910 1.61e-02 80 chrIV:16167520-16167600 6.54e-01 80 chrX:10690025-10690105 9.77e-01 80 chrI:14271472-14271552 1.33e-02 43_[+4(1.07e-05)]_29 chrIII:8806638-8806718 6.79e-04 64_[+1(4.35e-05)]_8 chrI:6094551-6094631 1.05e-01 6_[+2(4.14e-05)]_66 chrX:10395882-10395962 9.93e-03 29_[+3(1.08e-05)]_43 chrII:12055850-12055930 1.70e-01 80 chrII:12795398-12795478 2.89e-01 80 chrIII:5710852-5710932 7.01e-02 80 chrIV:12212341-12212421 2.77e-01 80 chrX:15842644-15842724 9.94e-01 80 chrIII:5506206-5506286 4.51e-02 80 chrX:15860773-15860853 5.88e-02 80 chrX:10647805-10647885 4.74e-01 80 chrX:12630780-12630860 4.69e-01 80 chrX:11813856-11813936 9.99e-01 80 chrII:15193029-15193109 1.38e-01 80 chrII:7319696-7319776 9.57e-02 80 chrI:7085981-7086061 6.75e-01 80 chrV:3633508-3633588 9.00e-01 80 chrX:10778883-10778963 9.83e-01 80 chrX:11410035-11410115 9.47e-01 80 chrII:4706520-4706600 1.19e-01 80 chrIII:13542827-13542907 9.35e-01 80 chrIII:9783164-9783244 4.87e-01 80 chrIV:9438875-9438955 4.26e-01 80 chrX:10778143-10778223 9.72e-01 80 chrX:10018461-10018541 4.69e-02 80 chrIV:13083136-13083216 4.64e-02 80 chrII:11926608-11926688 3.62e-01 80 chrIII:13719508-13719588 5.59e-01 80 chrII:7685010-7685090 2.50e-01 80 chrX:9378734-9378814 3.48e-02 80 chrX:2970285-2970365 4.81e-02 80 chrI:8302041-8302121 1.29e-01 26_[+1(4.35e-05)]_46 chrI:5314696-5314776 2.85e-01 39_[+1(4.35e-05)]_33 chrI:7016968-7017048 9.34e-01 80 chrX:10686597-10686677 1.31e-01 80 chrI:9333248-9333328 9.99e-01 80 chrII:7100845-7100925 5.65e-01 80 chrV:12038380-12038460 1.18e-01 80 chrIII:5920149-5920229 6.11e-01 80 chrX:15311299-15311379 4.08e-01 80 chrI:13060465-13060545 2.63e-02 80 chrI:10123412-10123492 1.09e-01 80 chrI:10407579-10407659 7.18e-01 80 chrV:5410852-5410932 7.40e-01 80 chrI:3826659-3826739 4.42e-01 80 chrIV:5805633-5805713 2.40e-02 80 chrII:1371725-1371805 8.31e-01 80 chrX:1451985-1452065 9.70e-01 80 chrX:10687409-10687489 4.13e-01 80 chrI:5372435-5372515 9.31e-01 80 chrIII:3902794-3902874 3.23e-02 80 chrI:8801880-8801960 2.11e-01 80 chrII:5341232-5341312 5.39e-01 80 chrX:15268272-15268352 3.04e-01 80 chrIV:2770975-2771055 9.11e-01 80 chrII:4719146-4719226 9.03e-01 80 chrII:8130898-8130978 7.23e-02 40_[+1(4.35e-05)]_32 chrIII:7145557-7145637 1.04e-01 80 chrI:7015743-7015823 3.21e-03 2_[+1(4.35e-05)]_70 chrV:8043497-8043577 6.70e-01 80 chrIII:10711392-10711472 8.56e-01 80 chrI:12041925-12042005 1.62e-01 12_[+2(9.62e-05)]_24_[+2(4.14e-05)]_\ 28 chrIV:1867054-1867134 1.21e-01 80 chrIV:13893292-13893372 3.84e-01 80 chrX:12504138-12504218 5.77e-01 80 chrV:6098772-6098852 9.88e-01 80 chrIV:7049062-7049142 2.60e-01 80 chrI:9101006-9101086 6.24e-01 80 chrIII:5653741-5653821 7.49e-01 80 chrX:13164358-13164438 7.10e-02 51_[+4(1.07e-05)]_21 chrX:13038963-13039043 2.47e-01 80 chrV:5587464-5587544 9.11e-01 80 chrV:9786657-9786737 6.75e-01 80 chrV:5838742-5838822 3.83e-01 80 chrV:9088965-9089045 6.14e-01 80 chrII:9128263-9128343 9.24e-01 80 chrIII:7374805-7374885 2.42e-01 70_[+2(9.62e-05)]_2 chrIV:17174265-17174345 9.69e-01 80 chrII:4857198-4857278 1.30e-01 80 chrV:14008468-14008548 5.13e-03 80 chrX:15877156-15877236 3.61e-01 80 chrX:15312224-15312304 3.67e-01 80 chrII:4745395-4745475 9.13e-01 80 chrI:10777417-10777497 3.39e-02 80 chrII:8789075-8789155 1.65e-01 80 chrIII:10763181-10763261 3.91e-01 80 chrIV:3653491-3653571 1.08e-01 80 chrX:15285644-15285724 1.72e-01 80 chrV:14366747-14366827 2.14e-04 37_[+5(9.59e-06)]_14_[+3(4.69e-06)]_\ 13 chrIII:13723360-13723440 7.38e-01 80 chrII:506186-506266 2.70e-02 3_[+1(4.35e-05)]_69 chrV:11225986-11226066 2.14e-01 80 chrII:4575655-4575735 9.82e-01 80 chrI:12732955-12733035 8.46e-02 80 chrX:7956450-7956530 5.14e-01 80 chrII:6891980-6892060 8.57e-01 80 chrI:1273899-1273979 4.11e-01 80 chrV:6426154-6426234 8.98e-01 80 chrI:8296705-8296785 9.99e-01 80 chrX:10480654-10480734 9.99e-01 80 chrIII:4562160-4562240 1.44e-01 80 chrV:11802582-11802662 9.67e-01 80 chrII:7347526-7347606 9.74e-01 80 chrX:16150346-16150426 7.08e-01 80 chrX:15878944-15879024 2.38e-01 80 chrII:12878572-12878652 7.01e-01 80 chrX:12201736-12201816 3.95e-01 80 chrII:1238051-1238131 2.20e-01 80 chrII:2028188-2028268 9.21e-02 80 chrII:12058417-12058497 8.80e-01 80 chrIII:13779498-13779578 4.68e-01 80 chrX:6041000-6041080 1.76e-03 80 chrII:549135-549215 1.04e-02 12_[+1(4.35e-05)]_12_[+4(9.13e-05)]_\ 40 chrV:5284763-5284843 9.98e-01 80 chrIII:6123751-6123831 3.82e-02 80 chrII:1239851-1239931 2.04e-01 80 chrX:8477543-8477623 6.66e-01 80 chrII:551484-551564 7.96e-01 80 chrII:11290559-11290639 1.05e-01 80 chrII:9211875-9211955 1.26e-01 80 chrX:15271632-15271712 2.69e-01 80 chrV:13649978-13650058 9.99e-01 80 chrII:8790102-8790182 8.70e-01 80 chrIII:7338828-7338908 1.85e-01 80 chrIII:3739887-3739967 5.67e-02 80 chrIII:11463940-11464020 8.54e-01 80 chrIV:2939578-2939658 2.31e-01 80 chrX:9952366-9952446 3.46e-01 80 chrII:1323287-1323367 2.41e-01 80 chrIV:4403746-4403826 1.50e-02 66_[+3(1.08e-05)]_6 chrV:19519584-19519664 7.13e-01 80 chrIII:6888637-6888717 4.84e-02 31_[+4(1.07e-05)]_41 chrIII:13065835-13065915 3.57e-01 80 chrIII:13346855-13346935 2.21e-02 80 chrI:9440640-9440720 6.84e-01 80 chrX:4146771-4146851 1.45e-02 52_[+2(4.14e-05)]_20 chrIII:13724642-13724722 4.37e-03 38_[+4(1.07e-05)]_34 chrV:12354606-12354686 8.47e-01 80 chrIII:5717669-5717749 1.92e-01 80 chrI:5616271-5616351 5.08e-01 80 chrIII:6447708-6447788 2.70e-01 80 chrII:4562772-4562852 9.27e-01 80 chrII:1148311-1148391 7.72e-02 28_[+2(9.62e-05)]_44 chrIII:8979125-8979205 4.27e-01 80 chrIII:10534273-10534353 3.39e-01 80 chrI:3834421-3834501 9.75e-01 80 chrI:8424568-8424648 3.97e-02 80 chrIV:13329876-13329956 2.51e-01 80 chrX:11340411-11340491 5.07e-01 80 chrX:8017416-8017496 5.38e-01 80 chrIV:4026161-4026241 5.28e-01 80 chrIV:7397635-7397715 1.55e-01 80 chrI:4001234-4001314 5.05e-01 80 chrV:9859819-9859899 8.73e-01 80 chrX:1445944-1446024 2.05e-01 80 chrI:13650996-13651076 1.01e-01 80 chrX:12501024-12501104 6.69e-02 80 chrI:14179844-14179924 9.93e-01 80 chrX:11240907-11240987 5.82e-01 80 chrIII:10093188-10093268 1.26e-01 80 chrIV:10778631-10778711 8.84e-01 80 chrI:12045378-12045458 5.05e-01 80 chrX:12503492-12503572 7.57e-01 80 chrIII:9509984-9510064 4.22e-01 39_[+2(9.62e-05)]_33 chrIII:4654023-4654103 6.22e-01 80 chrX:6252413-6252493 6.94e-01 80 chrIII:7387517-7387597 7.02e-02 6_[+1(4.35e-05)]_66 chrX:6808724-6808804 6.36e-01 80 chrIII:6144660-6144740 7.72e-03 [+1(4.35e-05)]_72 chrX:17545645-17545725 6.40e-01 80 chrIV:13388904-13388984 8.59e-02 80 chrIV:3370783-3370863 4.14e-01 80 chrIV:8529197-8529277 3.00e-01 80 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (5) found. ******************************************************************************** CPU: c27n08.farnam.hpc.yale.internal ********************************************************************************