******************************************************************************** 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/fly/fasta/RankLinear8.0_60/ab.fasta CONTROL SEQUENCES= --none-- ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ chr2L:11229359-11229479 1.0000 120 chr2L:15912554-15912674 1.0000 120 chr3R:14722365-14722485 1.0000 120 chr2L:2203244-2203364 1.0000 120 chr2R:23713275-23713395 1.0000 120 chr3L:17352909-17353029 1.0000 120 chr2L:11203731-11203851 1.0000 120 chr2L:12010634-12010754 1.0000 120 chr2R:17436507-17436627 1.0000 120 chr2L:1428159-1428279 1.0000 120 chr2L:11221118-11221238 1.0000 120 chr3R:8171617-8171737 1.0000 120 chr2R:24292872-24292992 1.0000 120 chr3L:6742414-6742534 1.0000 120 chr3R:12369299-12369419 1.0000 120 chr3R:4804999-4805119 1.0000 120 chr2R:7070872-7070992 1.0000 120 chr3R:5066727-5066847 1.0000 120 chr3R:6426401-6426521 1.0000 120 chr2L:12010835-12010955 1.0000 120 chr2L:2200329-2200449 1.0000 120 chr2R:6158012-6158132 1.0000 120 chr2L:18327253-18327373 1.0000 120 chr3L:18771859-18771979 1.0000 120 chr2R:24942814-24942934 1.0000 120 chrX:17830441-17830561 1.0000 120 chr2L:2162212-2162332 1.0000 120 chrX:2136469-2136589 1.0000 120 chr2R:18351714-18351834 1.0000 120 chr2L:16533985-16534105 1.0000 120 chrX:20507829-20507949 1.0000 120 chr3R:25490487-25490607 1.0000 120 chr3L:6189697-6189817 1.0000 120 chr3R:5685713-5685833 1.0000 120 chr2R:19451177-19451297 1.0000 120 chr2L:4218967-4219087 1.0000 120 chr2L:8541647-8541767 1.0000 120 chrX:21280909-21281029 1.0000 120 chr2L:11807169-11807289 1.0000 120 chr2L:10221081-10221201 1.0000 120 chr2L:11229590-11229710 1.0000 120 chr3R:26980485-26980605 1.0000 120 chr3R:25050751-25050871 1.0000 120 chr2L:14021771-14021891 1.0000 120 chr3R:26888447-26888567 1.0000 120 chr3L:3852991-3853111 1.0000 120 chr3L:4254307-4254427 1.0000 120 chr3R:14738871-14738991 1.0000 120 chr2R:18834759-18834879 1.0000 120 chr3R:16099850-16099970 1.0000 120 chr2R:7246859-7246979 1.0000 120 chr3R:5659259-5659379 1.0000 120 chr3L:11533986-11534106 1.0000 120 chr3R:26099383-26099503 1.0000 120 chr2L:11209046-11209166 1.0000 120 chr3L:1794556-1794676 1.0000 120 chrX:11137002-11137122 1.0000 120 chr3L:17644419-17644539 1.0000 120 chr2L:429816-429936 1.0000 120 chr3L:246694-246814 1.0000 120 chr3L:10737138-10737258 1.0000 120 chr3R:28599653-28599773 1.0000 120 chr3R:15093226-15093346 1.0000 120 chr2R:8572694-8572814 1.0000 120 chrX:12665260-12665380 1.0000 120 chr3L:12468165-12468285 1.0000 120 chr3R:17053957-17054077 1.0000 120 chr3L:626806-626926 1.0000 120 chr3R:9352880-9353000 1.0000 120 chrX:3862425-3862545 1.0000 120 chr2L:15248772-15248892 1.0000 120 chr2L:15913434-15913554 1.0000 120 chr2L:18944690-18944810 1.0000 120 chr2L:11192825-11192945 1.0000 120 chr3L:20395337-20395457 1.0000 120 chr3L:7867426-7867546 1.0000 120 chr2L:11971011-11971131 1.0000 120 chr3R:16250115-16250235 1.0000 120 chr3R:16748692-16748812 1.0000 120 chr3L:18759316-18759436 1.0000 120 chr2R:6878494-6878614 1.0000 120 chr3R:27245260-27245380 1.0000 120 chr2L:7641768-7641888 1.0000 120 chr3R:26536330-26536450 1.0000 120 chrX:3134421-3134541 1.0000 120 chr2L:18590797-18590917 1.0000 120 chr2R:15848053-15848173 1.0000 120 chr3R:29039754-29039874 1.0000 120 chr2L:18328901-18329021 1.0000 120 chr3L:6264591-6264711 1.0000 120 chr2L:14394644-14394764 1.0000 120 chr2R:24531505-24531625 1.0000 120 chr2L:2162012-2162132 1.0000 120 chr2R:23554578-23554698 1.0000 120 chr3L:6816300-6816420 1.0000 120 chr2R:13584561-13584681 1.0000 120 chr2L:1428372-1428492 1.0000 120 chr2R:22174675-22174795 1.0000 120 chr2L:15751124-15751244 1.0000 120 chr3R:5060974-5061094 1.0000 120 chr4:696780-696900 1.0000 120 chr3L:3665423-3665543 1.0000 120 chr2R:11275890-11276010 1.0000 120 chr2L:3776080-3776200 1.0000 120 chr2L:11206797-11206917 1.0000 120 chr2R:23383394-23383514 1.0000 120 chrX:12469798-12469918 1.0000 120 chr3R:9226980-9227100 1.0000 120 chr2L:2177715-2177835 1.0000 120 chr3L:4239590-4239710 1.0000 120 chrX:5517016-5517136 1.0000 120 chr3L:628223-628343 1.0000 120 chr3R:26052676-26052796 1.0000 120 chr2R:24539713-24539833 1.0000 120 chr3R:21580173-21580293 1.0000 120 chr3R:19118653-19118773 1.0000 120 chr2R:14484962-14485082 1.0000 120 chr3R:23921370-23921490 1.0000 120 chr3R:30601861-30601981 1.0000 120 chr2L:13833075-13833195 1.0000 120 chr3R:30796877-30796997 1.0000 120 chr3L:5185224-5185344 1.0000 120 chr3R:14016952-14017072 1.0000 120 chr3R:5856485-5856605 1.0000 120 chr2L:16887940-16888060 1.0000 120 chr2L:12011980-12012100 1.0000 120 chrX:2536263-2536383 1.0000 120 chrX:14602691-14602811 1.0000 120 chrX:3086006-3086126 1.0000 120 chr3L:9899152-9899272 1.0000 120 chr2R:22686130-22686250 1.0000 120 chr2R:12605681-12605801 1.0000 120 chr2R:7474282-7474402 1.0000 120 chr2L:6088480-6088600 1.0000 120 chr2R:24657163-24657283 1.0000 120 chr2L:5543183-5543303 1.0000 120 chrX:7703000-7703120 1.0000 120 chr3L:3070646-3070766 1.0000 120 chr2L:161865-161985 1.0000 120 chr2R:7492580-7492700 1.0000 120 chr2R:24343589-24343709 1.0000 120 chr2L:16272886-16273006 1.0000 120 chr2R:10475491-10475611 1.0000 120 chr3R:29763284-29763404 1.0000 120 chrX:14839741-14839861 1.0000 120 chr2L:11209251-11209371 1.0000 120 chr2L:14094788-14094908 1.0000 120 chr3L:7435128-7435248 1.0000 120 chr2R:14429845-14429965 1.0000 120 chrX:2533966-2534086 1.0000 120 chr3R:16241528-16241648 1.0000 120 chrX:11454393-11454513 1.0000 120 chr3L:17016040-17016160 1.0000 120 chr3L:628430-628550 1.0000 120 chr3L:17010116-17010236 1.0000 120 chr3L:11417277-11417397 1.0000 120 chr2R:13584289-13584409 1.0000 120 chr3R:14025135-14025255 1.0000 120 chr2R:12980580-12980700 1.0000 120 chr2R:11600810-11600930 1.0000 120 chr3R:17943516-17943636 1.0000 120 chr3L:223321-223441 1.0000 120 chr2R:18326650-18326770 1.0000 120 chr2R:24748944-24749064 1.0000 120 chrX:19667022-19667142 1.0000 120 chr3R:28887996-28888116 1.0000 120 chr2R:7278075-7278195 1.0000 120 chr3L:3326257-3326377 1.0000 120 chrX:17531967-17532087 1.0000 120 chr2L:5256137-5256257 1.0000 120 chr3R:29591556-29591676 1.0000 120 chrX:6316897-6317017 1.0000 120 chr2L:3813427-3813547 1.0000 120 chr2L:14122895-14123015 1.0000 120 chr3R:14706995-14707115 1.0000 120 chrX:13404339-13404459 1.0000 120 chr2R:17801031-17801151 1.0000 120 chr2L:3872419-3872539 1.0000 120 chr3R:10560650-10560770 1.0000 120 chrX:19663137-19663257 1.0000 120 chr2L:14500591-14500711 1.0000 120 chr3L:1740215-1740335 1.0000 120 chr2R:11197332-11197452 1.0000 120 chr2R:7395959-7396079 1.0000 120 chr3R:14473713-14473833 1.0000 120 chr2L:2197132-2197252 1.0000 120 chr3L:14982732-14982852 1.0000 120 chr2L:11269059-11269179 1.0000 120 chr3R:24962589-24962709 1.0000 120 chr3R:15793474-15793594 1.0000 120 chr3R:19644410-19644530 1.0000 120 chrX:7703759-7703879 1.0000 120 chr3R:29122905-29123025 1.0000 120 chr2L:7333247-7333367 1.0000 120 chr3R:8305366-8305486 1.0000 120 chr3R:8212711-8212831 1.0000 120 chr3R:9630740-9630860 1.0000 120 chr3R:24169549-24169669 1.0000 120 chr2R:18292624-18292744 1.0000 120 chr3R:21188817-21188937 1.0000 120 chr2L:11498946-11499066 1.0000 120 chr3L:10856601-10856721 1.0000 120 chr2L:14372486-14372606 1.0000 120 chr3R:27677350-27677470 1.0000 120 chr2L:3303188-3303308 1.0000 120 chr2R:19621889-19622009 1.0000 120 chr3R:31381403-31381523 1.0000 120 chr2R:19452415-19452535 1.0000 120 chr3L:10737337-10737457 1.0000 120 chr3R:21017608-21017728 1.0000 120 chr3R:21487901-21488021 1.0000 120 chr3R:10684435-10684555 1.0000 120 chr3R:21614991-21615111 1.0000 120 chr3L:1479434-1479554 1.0000 120 chr2L:14995708-14995828 1.0000 120 chr2L:16816430-16816550 1.0000 120 chr3L:13862543-13862663 1.0000 120 chr3R:13381983-13382103 1.0000 120 chrX:2070781-2070901 1.0000 120 chr3R:4659748-4659868 1.0000 120 chr2R:5974472-5974592 1.0000 120 chr3R:17401419-17401539 1.0000 120 chr2L:846295-846415 1.0000 120 chr3R:5061174-5061294 1.0000 120 chr2R:13579788-13579908 1.0000 120 chr2L:2878969-2879089 1.0000 120 chr3R:16869353-16869473 1.0000 120 chr3R:27282477-27282597 1.0000 120 chr2R:10874718-10874838 1.0000 120 chr2R:19205430-19205550 1.0000 120 chrX:13383867-13383987 1.0000 120 chr2R:17872000-17872120 1.0000 120 chr2R:23377025-23377145 1.0000 120 chr3L:12091464-12091584 1.0000 120 chr3R:4378943-4379063 1.0000 120 chr2R:20623419-20623539 1.0000 120 chr2L:1634146-1634266 1.0000 120 chrX:2083263-2083383 1.0000 120 chr3R:9598264-9598384 1.0000 120 chr2R:16338545-16338665 1.0000 120 chr3R:5862358-5862478 1.0000 120 chrX:18405855-18405975 1.0000 120 chrX:1879689-1879809 1.0000 120 chr3L:8153363-8153483 1.0000 120 chr3R:9881548-9881668 1.0000 120 chr3L:9023693-9023813 1.0000 120 chr3L:21539454-21539574 1.0000 120 chrX:2270742-2270862 1.0000 120 chr3R:11210119-11210239 1.0000 120 chr3R:4989689-4989809 1.0000 120 ******************************************************************************** ******************************************************************************** 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/fly/inference_raw/MEME/RankLinear8.0_60_ab/ -dna -nmotifs 5 -w 8 -maxsize 250000 -nostatus ../result/final_prediction/fly/fasta/RankLinear8.0_60/ab.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= 30000 N= 250 sample: seed= 0 hsfrac= 0 searchsize= 30000 norand= no csites= 1000 Letter frequencies in dataset: A 0.289 C 0.216 G 0.208 T 0.288 Background letter frequencies (from file dataset with add-one prior applied): A 0.289 C 0.216 G 0.208 T 0.288 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF CGCACACW MEME-1 width = 8 sites = 42 llr = 354 E-value = 1.3e-003 ******************************************************************************** -------------------------------------------------------------------------------- Motif CGCACACW MEME-1 Description -------------------------------------------------------------------------------- Simplified A :::8:8:6 pos.-specific C 9:a:91a: probability G :a:1:1:: matrix T 1:::1::4 bits 2.3 * 2.0 ** * 1.8 ** * * 1.6 *** * * Relative 1.4 *** * * Entropy 1.1 *** *** (12.2 bits) 0.9 ******* 0.7 ******** 0.5 ******** 0.2 ******** 0.0 -------- Multilevel CGCACACA consensus T sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CGCACACW MEME-1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr2R:19621889-19622009 2 1.09e-05 A CGCACACA TAAGTGCACT chr2L:2197132-2197252 18 1.09e-05 AATATGCCTA CGCACACA AGGAAACGAG chr2R:11197332-11197452 68 1.09e-05 ctcacactcg cgcacaca cacaGGCACG chr3R:16241528-16241648 46 1.09e-05 CACAGATACA CGCACACA CAGCGGCGAG chrX:14839741-14839861 71 1.09e-05 TCAGAATGCA CGCACACA CTAAGGGTTA chr2L:15913434-15913554 5 1.09e-05 CGTG CGCACACA ATCATTATCT chr3L:626806-626926 9 1.09e-05 CTcacaca cgcacaca cacacagcgg chr3L:12468165-12468285 47 1.09e-05 ACACTATGCG CGCACACA AATCAAACAA chr2R:19451177-19451297 92 1.09e-05 GACACACACA CGCACACA ACTTGGTATA chr3R:16869353-16869473 74 2.18e-05 AAACGCATTA CGCACACT TACAACGCTT chr3R:8212711-8212831 69 2.18e-05 TAAAAGCCTT CGCACACT TACATTTTTA chr3L:3070646-3070766 31 2.18e-05 CTCTTTCGCT CGCACACT AAGTATGGCA chr2L:11229359-11229479 69 2.18e-05 GTAGATACGA CGCACACT TACAGGTCGC chr2R:14429845-14429965 10 3.76e-05 acacgcaca cgcacgca cgccgatcgc chr3R:14016952-14017072 55 3.76e-05 CCTTGCACCG CGCGCACA AACTTCGTAG chr2R:22174675-22174795 1 3.76e-05 . CGCGCACA ACAGAGATGA chr2L:12010634-12010754 37 3.76e-05 TTAGAAGCAG CGCACGCA GGTGCGAGCG chrX:2083263-2083383 3 5.21e-05 CC TGCACACA TGATCTATGA chr3R:21614991-21615111 54 5.21e-05 ATTTAATATT TGCACACA ATTTTCCACA chr2R:7395959-7396079 17 5.21e-05 GGCGAAAATG TGCACACA ATTTTATCGC chr3L:18759316-18759436 25 5.21e-05 TCGTATCACG TGCACACA CACCAGCGCA chr2R:17436507-17436627 39 5.21e-05 AAGTCACACA TGCACACA TGTACGGGTG chr3R:16099850-16099970 50 6.03e-05 CCCTCCCCCT CGCACCCA CAGTCTGGCC chrX:19667022-19667142 112 7.60e-05 TGGGCCCCCG CGCGCACT G chr2L:18327253-18327373 12 7.60e-05 CTCTCCCTCT CGCACGCT CGCTTTGCGC chr2R:6158012-6158132 59 7.60e-05 CTCCACTGTG CGCGCACT TGGCCAAACA chr2L:15912554-15912674 21 7.60e-05 GAGTGCATCT CGCACGCT CCACTCGAGT chr2R:19452415-19452535 38 1.13e-04 AAACATAGGA TGCACACT GTAGAAACTA chr3L:10856601-10856721 15 1.13e-04 TTACAAGCCA CGCATACA AACGCAAACG chr2L:12011980-12012100 20 1.13e-04 ATTTATAAAC CGCATACA CCCATTTCGC chr2L:18590797-18590917 90 1.13e-04 GATAGCATCG CGCATACA CCAGCTTTTT chr3R:5862358-5862478 91 1.21e-04 CCAGTTGCTG CGCACCCT TACCAACACT chr2R:23383394-23383514 12 1.21e-04 TGACCGTAGG CGCACCCT TAAATAATAC chr2R:12980580-12980700 35 1.51e-04 AACAACCGAC CGCACACG TCCGTTCGCT chr3L:17016040-17016160 11 1.51e-04 ACCGAAAAAG CGCTCACA GCGAAACGCC chr2R:13584561-13584681 59 1.51e-04 TTTTAACAGG CGCACAGA ATTAGCAGCA chr2L:14995708-14995828 70 1.73e-04 CACCCCTTTC CGCCCACT ATACCCCTCT chr3R:29591556-29591676 9 1.73e-04 TAAATTAA CGCATACT TAAACTGGCG chr2R:24531505-24531625 15 1.73e-04 TTGAATTTCC CGCCCACT GAATGGAAAC chr3R:17053957-17054077 30 1.95e-04 ACTATCAATC CGCACAGT TAGCGCTTCG chr3L:6742414-6742534 36 1.95e-04 ATAGCCGAAC CGCTCACT TTTTCACGTT chr2L:3872419-3872539 90 2.48e-04 CAAGCCATGC CACACACA GCACTAGCAA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CGCACACW MEME-1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr2R:19621889-19622009 1.1e-05 1_[+1]_111 chr2L:2197132-2197252 1.1e-05 17_[+1]_95 chr2R:11197332-11197452 1.1e-05 67_[+1]_45 chr3R:16241528-16241648 1.1e-05 45_[+1]_67 chrX:14839741-14839861 1.1e-05 70_[+1]_42 chr2L:15913434-15913554 1.1e-05 4_[+1]_108 chr3L:626806-626926 1.1e-05 8_[+1]_104 chr3L:12468165-12468285 1.1e-05 46_[+1]_66 chr2R:19451177-19451297 1.1e-05 91_[+1]_21 chr3R:16869353-16869473 2.2e-05 73_[+1]_39 chr3R:8212711-8212831 2.2e-05 68_[+1]_44 chr3L:3070646-3070766 2.2e-05 30_[+1]_82 chr2L:11229359-11229479 2.2e-05 68_[+1]_44 chr2R:14429845-14429965 3.8e-05 9_[+1]_103 chr3R:14016952-14017072 3.8e-05 54_[+1]_58 chr2R:22174675-22174795 3.8e-05 [+1]_112 chr2L:12010634-12010754 3.8e-05 36_[+1]_76 chrX:2083263-2083383 5.2e-05 2_[+1]_110 chr3R:21614991-21615111 5.2e-05 53_[+1]_59 chr2R:7395959-7396079 5.2e-05 16_[+1]_96 chr3L:18759316-18759436 5.2e-05 24_[+1]_88 chr2R:17436507-17436627 5.2e-05 38_[+1]_74 chr3R:16099850-16099970 6e-05 49_[+1]_63 chrX:19667022-19667142 7.6e-05 111_[+1]_1 chr2L:18327253-18327373 7.6e-05 11_[+1]_101 chr2R:6158012-6158132 7.6e-05 58_[+1]_54 chr2L:15912554-15912674 7.6e-05 20_[+1]_92 chr2R:19452415-19452535 0.00011 37_[+1]_75 chr3L:10856601-10856721 0.00011 14_[+1]_98 chr2L:12011980-12012100 0.00011 19_[+1]_93 chr2L:18590797-18590917 0.00011 89_[+1]_23 chr3R:5862358-5862478 0.00012 90_[+1]_22 chr2R:23383394-23383514 0.00012 11_[+1]_101 chr2R:12980580-12980700 0.00015 34_[+1]_78 chr3L:17016040-17016160 0.00015 10_[+1]_102 chr2R:13584561-13584681 0.00015 58_[+1]_54 chr2L:14995708-14995828 0.00017 69_[+1]_43 chr3R:29591556-29591676 0.00017 8_[+1]_104 chr2R:24531505-24531625 0.00017 14_[+1]_98 chr3R:17053957-17054077 0.00019 29_[+1]_83 chr3L:6742414-6742534 0.00019 35_[+1]_77 chr2L:3872419-3872539 0.00025 89_[+1]_23 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CGCACACW MEME-1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF CGCACACW width=8 seqs=42 chr2R:19621889-19622009 ( 2) CGCACACA 1 chr2L:2197132-2197252 ( 18) CGCACACA 1 chr2R:11197332-11197452 ( 68) CGCACACA 1 chr3R:16241528-16241648 ( 46) CGCACACA 1 chrX:14839741-14839861 ( 71) CGCACACA 1 chr2L:15913434-15913554 ( 5) CGCACACA 1 chr3L:626806-626926 ( 9) CGCACACA 1 chr3L:12468165-12468285 ( 47) CGCACACA 1 chr2R:19451177-19451297 ( 92) CGCACACA 1 chr3R:16869353-16869473 ( 74) CGCACACT 1 chr3R:8212711-8212831 ( 69) CGCACACT 1 chr3L:3070646-3070766 ( 31) CGCACACT 1 chr2L:11229359-11229479 ( 69) CGCACACT 1 chr2R:14429845-14429965 ( 10) CGCACGCA 1 chr3R:14016952-14017072 ( 55) CGCGCACA 1 chr2R:22174675-22174795 ( 1) CGCGCACA 1 chr2L:12010634-12010754 ( 37) CGCACGCA 1 chrX:2083263-2083383 ( 3) TGCACACA 1 chr3R:21614991-21615111 ( 54) TGCACACA 1 chr2R:7395959-7396079 ( 17) TGCACACA 1 chr3L:18759316-18759436 ( 25) TGCACACA 1 chr2R:17436507-17436627 ( 39) TGCACACA 1 chr3R:16099850-16099970 ( 50) CGCACCCA 1 chrX:19667022-19667142 ( 112) CGCGCACT 1 chr2L:18327253-18327373 ( 12) CGCACGCT 1 chr2R:6158012-6158132 ( 59) CGCGCACT 1 chr2L:15912554-15912674 ( 21) CGCACGCT 1 chr2R:19452415-19452535 ( 38) TGCACACT 1 chr3L:10856601-10856721 ( 15) CGCATACA 1 chr2L:12011980-12012100 ( 20) CGCATACA 1 chr2L:18590797-18590917 ( 90) CGCATACA 1 chr3R:5862358-5862478 ( 91) CGCACCCT 1 chr2R:23383394-23383514 ( 12) CGCACCCT 1 chr2R:12980580-12980700 ( 35) CGCACACG 1 chr3L:17016040-17016160 ( 11) CGCTCACA 1 chr2R:13584561-13584681 ( 59) CGCACAGA 1 chr2L:14995708-14995828 ( 70) CGCCCACT 1 chr3R:29591556-29591676 ( 9) CGCATACT 1 chr2R:24531505-24531625 ( 15) CGCCCACT 1 chr3R:17053957-17054077 ( 30) CGCACAGT 1 chr3L:6742414-6742534 ( 36) CGCTCACT 1 chr2L:3872419-3872539 ( 90) CACACACA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CGCACACW MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 28250 bayes= 9.69676 E= 1.3e-003 -1204 199 -1204 -101 -360 -1204 223 -1204 -1204 221 -1204 -1204 149 -218 -112 -260 -1204 207 -1204 -160 153 -159 -112 -1204 -1204 214 -212 -1204 104 -1204 -312 40 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CGCACACW MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 42 E= 1.3e-003 0.000000 0.857143 0.000000 0.142857 0.023810 0.000000 0.976190 0.000000 0.000000 1.000000 0.000000 0.000000 0.809524 0.047619 0.095238 0.047619 0.000000 0.904762 0.000000 0.095238 0.833333 0.071429 0.095238 0.000000 0.000000 0.952381 0.047619 0.000000 0.595238 0.000000 0.023810 0.380952 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CGCACACW MEME-1 regular expression -------------------------------------------------------------------------------- CGCACAC[AT] -------------------------------------------------------------------------------- Time 7.35 secs. ******************************************************************************** ******************************************************************************** MOTIF CTCBCTCT MEME-2 width = 8 sites = 28 llr = 256 E-value = 2.1e-001 ******************************************************************************** -------------------------------------------------------------------------------- Motif CTCBCTCT MEME-2 Description -------------------------------------------------------------------------------- Simplified A :::::::1 pos.-specific C a:a3a1a1 probability G :::4:::1 matrix T :a:3:9:7 bits 2.3 * * * * 2.0 * * * * 1.8 *** * * 1.6 *** * * Relative 1.4 *** *** Entropy 1.1 *** *** (13.2 bits) 0.9 *** *** 0.7 ******** 0.5 ******** 0.2 ******** 0.0 -------- Multilevel CTCGCTCT consensus C sequence T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTCBCTCT MEME-2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr3L:10856601-10856721 58 1.08e-05 CCctctctct ctcgctct ctctctctct chr2L:2197132-2197252 101 1.08e-05 TACCTTTGCG CTCGCTCT GGCGTGGTGA chr2L:161865-161985 43 1.08e-05 AGCTGGCTAT CTCGCTCT AGCAACCACG chr2L:6088480-6088600 93 1.08e-05 CGCGTGTTGG CTCGCTCT TCTTCTTCTT chrX:5517016-5517136 105 1.08e-05 CCATGTGTTG CTCGctct ctgtctct chr3R:16250115-16250235 100 1.08e-05 TTTGCCctcg ctcgctct cttcttcttc chr3L:7867426-7867546 54 1.08e-05 actctgctct ctcgctct ctctTTTTGG chr3L:12468165-12468285 1 1.08e-05 . CTCGCTCT TCTGCGCGAG chr3L:10737138-10737258 44 1.08e-05 AGCAAACTCT CTCGCTCT CTCACGAGAG chr3R:14722365-14722485 91 1.08e-05 AGCGCTCTCG CTCGCTCT CCTTTGGCTC chr2R:24657163-24657283 92 2.20e-05 TGATTTATGC CTCCCTCT TTTTCTCAGT chr2R:24942814-24942934 112 2.20e-05 GAGATCCACG CTCCCTCT A chr2L:18327253-18327373 4 2.20e-05 TCT CTCCCTCT CGCACGCTCG chr2L:14995708-14995828 84 3.70e-05 CACTATACCC CTCTCTCT AACACCTTTG chr2L:3303188-3303308 98 3.70e-05 TTGTTTACGA CTCTCTCT TCTGCGGGGG chr3L:3070646-3070766 17 3.70e-05 AGTTTGCTCT CTCTCTCT TTCGCTCGCA chr3R:9226980-9227100 111 3.70e-05 CCCTACATAT CTCTCTCT TT chr2R:18351714-18351834 101 3.70e-05 TTGTGTATCT CTCTCTCT CTTTCGCTTT chr2L:11209251-11209371 45 4.51e-05 AATTTCATAC CTCGCTCC AATGGAAGCG chr3R:16099850-16099970 38 5.36e-05 TACTGTCTGT CTCCCTCC CCCTCGCACC chr2R:22686130-22686250 44 8.07e-05 GTCCCCCGCC CTCTCTCC TGCTGCTTAT chr2R:11197332-11197452 50 1.08e-04 acgcaacagt ctcgctca ctcacactcg chr3R:10560650-10560770 44 1.08e-04 CTTCAAACCC CTCCCTCG TAATGCACGT chr2R:7246859-7246979 86 1.08e-04 CTCCACGATT CTCCCTCG AAATAAGCCA chr3R:6426401-6426521 64 1.08e-04 AGCCCCTCCC CTCCCCCT TCCTGTCTGC chr3R:4804999-4805119 107 1.08e-04 TGTGCCCTAC CTCCCCCT TTGAAA chr3L:5185224-5185344 93 1.63e-04 GCGCGTTTGG CTCTCTCA CTTGTTTTGC chr2L:1634146-1634266 81 1.69e-04 CAGTCTCTTT CTCCCCCC ATAATAACTA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTCBCTCT MEME-2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr3L:10856601-10856721 1.1e-05 57_[+2]_55 chr2L:2197132-2197252 1.1e-05 100_[+2]_12 chr2L:161865-161985 1.1e-05 42_[+2]_70 chr2L:6088480-6088600 1.1e-05 92_[+2]_20 chrX:5517016-5517136 1.1e-05 104_[+2]_8 chr3R:16250115-16250235 1.1e-05 99_[+2]_13 chr3L:7867426-7867546 1.1e-05 53_[+2]_59 chr3L:12468165-12468285 1.1e-05 [+2]_112 chr3L:10737138-10737258 1.1e-05 43_[+2]_69 chr3R:14722365-14722485 1.1e-05 90_[+2]_22 chr2R:24657163-24657283 2.2e-05 91_[+2]_21 chr2R:24942814-24942934 2.2e-05 111_[+2]_1 chr2L:18327253-18327373 2.2e-05 3_[+2]_109 chr2L:14995708-14995828 3.7e-05 83_[+2]_29 chr2L:3303188-3303308 3.7e-05 97_[+2]_15 chr3L:3070646-3070766 3.7e-05 16_[+2]_96 chr3R:9226980-9227100 3.7e-05 110_[+2]_2 chr2R:18351714-18351834 3.7e-05 100_[+2]_12 chr2L:11209251-11209371 4.5e-05 44_[+2]_68 chr3R:16099850-16099970 5.4e-05 37_[+2]_75 chr2R:22686130-22686250 8.1e-05 43_[+2]_69 chr2R:11197332-11197452 0.00011 49_[+2]_63 chr3R:10560650-10560770 0.00011 43_[+2]_69 chr2R:7246859-7246979 0.00011 85_[+2]_27 chr3R:6426401-6426521 0.00011 63_[+2]_49 chr3R:4804999-4805119 0.00011 106_[+2]_6 chr3L:5185224-5185344 0.00016 92_[+2]_20 chr2L:1634146-1634266 0.00017 80_[+2]_32 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTCBCTCT MEME-2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF CTCBCTCT width=8 seqs=28 chr3L:10856601-10856721 ( 58) CTCGCTCT 1 chr2L:2197132-2197252 ( 101) CTCGCTCT 1 chr2L:161865-161985 ( 43) CTCGCTCT 1 chr2L:6088480-6088600 ( 93) CTCGCTCT 1 chrX:5517016-5517136 ( 105) CTCGCTCT 1 chr3R:16250115-16250235 ( 100) CTCGCTCT 1 chr3L:7867426-7867546 ( 54) CTCGCTCT 1 chr3L:12468165-12468285 ( 1) CTCGCTCT 1 chr3L:10737138-10737258 ( 44) CTCGCTCT 1 chr3R:14722365-14722485 ( 91) CTCGCTCT 1 chr2R:24657163-24657283 ( 92) CTCCCTCT 1 chr2R:24942814-24942934 ( 112) CTCCCTCT 1 chr2L:18327253-18327373 ( 4) CTCCCTCT 1 chr2L:14995708-14995828 ( 84) CTCTCTCT 1 chr2L:3303188-3303308 ( 98) CTCTCTCT 1 chr3L:3070646-3070766 ( 17) CTCTCTCT 1 chr3R:9226980-9227100 ( 111) CTCTCTCT 1 chr2R:18351714-18351834 ( 101) CTCTCTCT 1 chr2L:11209251-11209371 ( 45) CTCGCTCC 1 chr3R:16099850-16099970 ( 38) CTCCCTCC 1 chr2R:22686130-22686250 ( 44) CTCTCTCC 1 chr2R:11197332-11197452 ( 50) CTCGCTCA 1 chr3R:10560650-10560770 ( 44) CTCCCTCG 1 chr2R:7246859-7246979 ( 86) CTCCCTCG 1 chr3R:6426401-6426521 ( 64) CTCCCCCT 1 chr3R:4804999-4805119 ( 107) CTCCCCCT 1 chr3L:5185224-5185344 ( 93) CTCTCTCA 1 chr2L:1634146-1634266 ( 81) CTCCCCCC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTCBCTCT MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 28250 bayes= 10.5834 E= 2.1e-001 -1145 221 -1145 -1145 -1145 -1145 -1145 180 -1145 221 -1145 -1145 -1145 58 105 -20 -1145 221 -1145 -1145 -1145 -101 -1145 163 -1145 221 -1145 -1145 -201 -59 -154 131 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTCBCTCT MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 28 E= 2.1e-001 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 0.321429 0.428571 0.250000 0.000000 1.000000 0.000000 0.000000 0.000000 0.107143 0.000000 0.892857 0.000000 1.000000 0.000000 0.000000 0.071429 0.142857 0.071429 0.714286 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTCBCTCT MEME-2 regular expression -------------------------------------------------------------------------------- CTC[GCT]CTCT -------------------------------------------------------------------------------- Time 13.53 secs. ******************************************************************************** ******************************************************************************** MOTIF GAGCGAGA MEME-3 width = 8 sites = 11 llr = 119 E-value = 6.1e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif GAGCGAGA MEME-3 Description -------------------------------------------------------------------------------- Simplified A :8:::a:9 pos.-specific C :2:a:::1 probability G a:a:a:a: matrix T :::::::: bits 2.3 * *** * 2.0 * *** * 1.8 * ***** 1.6 * ***** Relative 1.4 * ****** Entropy 1.1 ******** (15.7 bits) 0.9 ******** 0.7 ******** 0.5 ******** 0.2 ******** 0.0 -------- Multilevel GAGCGAGA consensus sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GAGCGAGA MEME-3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr3R:9881548-9881668 95 9.76e-06 TAAGCGGCCA GAGCGAGA TGGCAATAAA chr3L:10737337-10737457 95 9.76e-06 CAGAAGgaga gagcgaga cggagagtgt chr3R:27245260-27245380 1 9.76e-06 . GAGCGAGA CAGCATGGCA chr3L:10737138-10737258 67 9.76e-06 GAGAGAAAGA GAGCGAGA GTCGTTGcgc chr3L:18771859-18771979 60 9.76e-06 TTTCCACCAT GAGCGAGA GTGAGAGGGC chr2L:2200329-2200449 26 9.76e-06 GCAACGCTGC GAGCGAGA CAGCGATAGG chr2L:12010634-12010754 50 9.76e-06 ACGCAGGTGC GAGCGAGA CGAGCGTAGG chr3R:14722365-14722485 6 9.76e-06 GGCGC GAGCGAGA TGGAAGACAA chr2L:3303188-3303308 16 1.71e-05 CGAGGGGAGA GCGCGAGA GCGCCGCAAT chr3L:12468165-12468285 12 1.71e-05 TCGCTCTTCT GCGCGAGA GCGGGACAAC chr2R:23383394-23383514 40 2.43e-05 CTTCGCGGCA GAGCGAGC ACAGTCGGCG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GAGCGAGA MEME-3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr3R:9881548-9881668 9.8e-06 94_[+3]_18 chr3L:10737337-10737457 9.8e-06 94_[+3]_18 chr3R:27245260-27245380 9.8e-06 [+3]_112 chr3L:10737138-10737258 9.8e-06 66_[+3]_46 chr3L:18771859-18771979 9.8e-06 59_[+3]_53 chr2L:2200329-2200449 9.8e-06 25_[+3]_87 chr2L:12010634-12010754 9.8e-06 49_[+3]_63 chr3R:14722365-14722485 9.8e-06 5_[+3]_107 chr2L:3303188-3303308 1.7e-05 15_[+3]_97 chr3L:12468165-12468285 1.7e-05 11_[+3]_101 chr2R:23383394-23383514 2.4e-05 39_[+3]_73 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GAGCGAGA MEME-3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF GAGCGAGA width=8 seqs=11 chr3R:9881548-9881668 ( 95) GAGCGAGA 1 chr3L:10737337-10737457 ( 95) GAGCGAGA 1 chr3R:27245260-27245380 ( 1) GAGCGAGA 1 chr3L:10737138-10737258 ( 67) GAGCGAGA 1 chr3L:18771859-18771979 ( 60) GAGCGAGA 1 chr2L:2200329-2200449 ( 26) GAGCGAGA 1 chr2L:12010634-12010754 ( 50) GAGCGAGA 1 chr3R:14722365-14722485 ( 6) GAGCGAGA 1 chr2L:3303188-3303308 ( 16) GCGCGAGA 1 chr3L:12468165-12468285 ( 12) GCGCGAGA 1 chr2R:23383394-23383514 ( 40) GAGCGAGC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GAGCGAGA MEME-3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 28250 bayes= 11.6812 E= 6.1e+001 -1010 -1010 227 -1010 150 -25 -1010 -1010 -1010 -1010 227 -1010 -1010 221 -1010 -1010 -1010 -1010 227 -1010 179 -1010 -1010 -1010 -1010 -1010 227 -1010 165 -124 -1010 -1010 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GAGCGAGA MEME-3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 11 E= 6.1e+001 0.000000 0.000000 1.000000 0.000000 0.818182 0.181818 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 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.909091 0.090909 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GAGCGAGA MEME-3 regular expression -------------------------------------------------------------------------------- GAGCGAGA -------------------------------------------------------------------------------- Time 19.66 secs. ******************************************************************************** ******************************************************************************** MOTIF CAGTGSDG MEME-4 width = 8 sites = 16 llr = 158 E-value = 5.0e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif CAGTGSDG MEME-4 Description -------------------------------------------------------------------------------- Simplified A :a::::4: pos.-specific C a::::6:: probability G ::a:a43a matrix T :::a::3: bits 2.3 * * * * 2.0 * * * * 1.8 ***** * 1.6 ***** * Relative 1.4 ****** * Entropy 1.1 ****** * (14.3 bits) 0.9 ****** * 0.7 ****** * 0.5 ******** 0.2 ******** 0.0 -------- Multilevel CAGTGCAG consensus GG sequence T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CAGTGSDG MEME-4 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr3L:8153363-8153483 94 1.74e-05 TCATTCTTCT CAGTGCAG CGGCAGTAGC chr2L:14122895-14123015 112 1.74e-05 AATTAAACCG CAGTGCAG A chr2R:24657163-24657283 106 1.74e-05 CTCTTTTTCT CAGTGCAG CTCAAGC chrX:3086006-3086126 93 1.74e-05 TTTTTTCTCA CAGTGCAG CTTATCGGCT chr3R:27245260-27245380 81 1.74e-05 AGACAGTCGC CAGTGCAG TGCGTTGGGG chr3L:20395337-20395457 68 1.74e-05 AATACATTTC CAGTGCGG TTACATACAG chrX:13404339-13404459 65 3.41e-05 AGAGGAGCAG CAGTGGGG GCACCATATA chrX:14602691-14602811 90 3.41e-05 CTGAACATTT CAGTGGGG AGTCAACTGT chr3L:5185224-5185344 26 3.41e-05 AAAATTCGCA CAGTGGAG CAGAAATCAA chr2L:15751124-15751244 25 3.41e-05 attactcata cagtggag ggtatactag chrX:12665260-12665380 40 3.41e-05 CAGGCGTGCG CAGTGGGG CCCATTTACC chr2R:7246859-7246979 21 3.41e-05 CGTGACTCAG CAGTGGGG CAACCGCCGG chr2L:16816430-16816550 1 4.42e-05 . CAGTGCTG ACATGTTAGC chr2L:3813427-3813547 4 4.42e-05 GAA CAGTGCTG TAAAGGGACA chr3R:5856485-5856605 93 4.42e-05 GTTGCAGCAG CAGTGCTG CAAAACGCGA chrX:11137002-11137122 78 4.42e-05 GCAGCGCAAA CAGTGCTG GCAATCAGCC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CAGTGSDG MEME-4 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr3L:8153363-8153483 1.7e-05 93_[+4]_19 chr2L:14122895-14123015 1.7e-05 111_[+4]_1 chr2R:24657163-24657283 1.7e-05 105_[+4]_7 chrX:3086006-3086126 1.7e-05 92_[+4]_20 chr3R:27245260-27245380 1.7e-05 80_[+4]_32 chr3L:20395337-20395457 1.7e-05 67_[+4]_45 chrX:13404339-13404459 3.4e-05 64_[+4]_48 chrX:14602691-14602811 3.4e-05 89_[+4]_23 chr3L:5185224-5185344 3.4e-05 25_[+4]_87 chr2L:15751124-15751244 3.4e-05 24_[+4]_88 chrX:12665260-12665380 3.4e-05 39_[+4]_73 chr2R:7246859-7246979 3.4e-05 20_[+4]_92 chr2L:16816430-16816550 4.4e-05 [+4]_112 chr2L:3813427-3813547 4.4e-05 3_[+4]_109 chr3R:5856485-5856605 4.4e-05 92_[+4]_20 chrX:11137002-11137122 4.4e-05 77_[+4]_35 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CAGTGSDG MEME-4 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF CAGTGSDG width=8 seqs=16 chr3L:8153363-8153483 ( 94) CAGTGCAG 1 chr2L:14122895-14123015 ( 112) CAGTGCAG 1 chr2R:24657163-24657283 ( 106) CAGTGCAG 1 chrX:3086006-3086126 ( 93) CAGTGCAG 1 chr3R:27245260-27245380 ( 81) CAGTGCAG 1 chr3L:20395337-20395457 ( 68) CAGTGCGG 1 chrX:13404339-13404459 ( 65) CAGTGGGG 1 chrX:14602691-14602811 ( 90) CAGTGGGG 1 chr3L:5185224-5185344 ( 26) CAGTGGAG 1 chr2L:15751124-15751244 ( 25) CAGTGGAG 1 chrX:12665260-12665380 ( 40) CAGTGGGG 1 chr2R:7246859-7246979 ( 21) CAGTGGGG 1 chr2L:16816430-16816550 ( 1) CAGTGCTG 1 chr2L:3813427-3813547 ( 4) CAGTGCTG 1 chr3R:5856485-5856605 ( 93) CAGTGCTG 1 chrX:11137002-11137122 ( 78) CAGTGCTG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CAGTGSDG MEME-4 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 28250 bayes= 12.1076 E= 5.0e+002 -1064 221 -1064 -1064 179 -1064 -1064 -1064 -1064 -1064 227 -1064 -1064 -1064 -1064 179 -1064 -1064 227 -1064 -1064 154 85 -1064 60 -1064 59 -20 -1064 -1064 227 -1064 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CAGTGSDG MEME-4 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 16 E= 5.0e+002 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 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 0.625000 0.375000 0.000000 0.437500 0.000000 0.312500 0.250000 0.000000 0.000000 1.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CAGTGSDG MEME-4 regular expression -------------------------------------------------------------------------------- CAGTG[CG][AGT]G -------------------------------------------------------------------------------- Time 25.80 secs. ******************************************************************************** ******************************************************************************** MOTIF GCGGKGCG MEME-5 width = 8 sites = 7 llr = 77 E-value = 1.0e+004 ******************************************************************************** -------------------------------------------------------------------------------- Motif GCGGKGCG MEME-5 Description -------------------------------------------------------------------------------- Simplified A ::::1::: pos.-specific C :a::1:a: probability G a:aa3a:a matrix T ::::4::: bits 2.3 **** *** 2.0 **** *** 1.8 **** *** 1.6 **** *** Relative 1.4 **** *** Entropy 1.1 **** *** (15.9 bits) 0.9 **** *** 0.7 **** *** 0.5 **** *** 0.2 ******** 0.0 -------- Multilevel GCGGTGCG consensus G sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCGGKGCG MEME-5 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr3R:13381983-13382103 68 9.01e-06 TCGGACCTTT GCGGTGCG AGGCAACCCT chr2R:14484962-14485082 68 9.01e-06 GGGTTGGCAA GCGGGGCG Tggcgagggg chr3R:27245260-27245380 41 9.01e-06 CATGGTGTGA GCGGTGCG GCTAGTGTGA chr2L:12010835-12010955 42 9.01e-06 TCCACTGTGC GCGGTGCG GTGTGGTGTG chr3R:12369299-12369419 54 9.01e-06 GAAGCGCCCC GCGGGGCG TGGCAAGGTG chr2L:11807169-11807289 34 1.29e-05 GCGAGTACAG GCGGCGCG TCGATACAAG chr2R:10475491-10475611 38 1.82e-05 AGCACTCGGA GCGGAGCG CCGAGACGGA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCGGKGCG MEME-5 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr3R:13381983-13382103 9e-06 67_[+5]_45 chr2R:14484962-14485082 9e-06 67_[+5]_45 chr3R:27245260-27245380 9e-06 40_[+5]_72 chr2L:12010835-12010955 9e-06 41_[+5]_71 chr3R:12369299-12369419 9e-06 53_[+5]_59 chr2L:11807169-11807289 1.3e-05 33_[+5]_79 chr2R:10475491-10475611 1.8e-05 37_[+5]_75 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCGGKGCG MEME-5 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF GCGGKGCG width=8 seqs=7 chr3R:13381983-13382103 ( 68) GCGGTGCG 1 chr2R:14484962-14485082 ( 68) GCGGGGCG 1 chr3R:27245260-27245380 ( 41) GCGGTGCG 1 chr2L:12010835-12010955 ( 42) GCGGTGCG 1 chr3R:12369299-12369419 ( 54) GCGGGGCG 1 chr2L:11807169-11807289 ( 34) GCGGCGCG 1 chr2R:10475491-10475611 ( 38) GCGGAGCG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCGGKGCG MEME-5 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 28250 bayes= 13.2008 E= 1.0e+004 -945 -945 227 -945 -945 221 -945 -945 -945 -945 227 -945 -945 -945 227 -945 -101 -59 46 57 -945 -945 227 -945 -945 221 -945 -945 -945 -945 227 -945 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCGGKGCG MEME-5 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 7 E= 1.0e+004 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 0.142857 0.142857 0.285714 0.428571 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCGGKGCG MEME-5 regular expression -------------------------------------------------------------------------------- GCGG[TG]GCG -------------------------------------------------------------------------------- Time 31.95 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr2L:11229359-11229479 7.65e-02 68_[+1(2.18e-05)]_44 chr2L:15912554-15912674 2.50e-03 20_[+1(7.60e-05)]_92 chr3R:14722365-14722485 1.93e-04 5_[+3(9.76e-06)]_77_[+2(1.08e-05)]_\ 22 chr2L:2203244-2203364 4.29e-02 120 chr2R:23713275-23713395 5.38e-01 120 chr3L:17352909-17353029 5.35e-01 120 chr2L:11203731-11203851 7.53e-01 120 chr2L:12010634-12010754 2.06e-04 36_[+1(3.76e-05)]_5_[+3(9.76e-06)]_\ 63 chr2R:17436507-17436627 9.66e-02 38_[+1(5.21e-05)]_74 chr2L:1428159-1428279 4.19e-01 120 chr2L:11221118-11221238 2.98e-01 120 chr3R:8171617-8171737 3.79e-01 73_[+3(6.33e-05)]_39 chr2R:24292872-24292992 9.63e-01 120 chr3L:6742414-6742534 1.66e-01 120 chr3R:12369299-12369419 5.28e-03 53_[+5(9.01e-06)]_59 chr3R:4804999-4805119 6.80e-02 120 chr2R:7070872-7070992 8.04e-01 120 chr3R:5066727-5066847 7.67e-01 120 chr3R:6426401-6426521 1.90e-01 120 chr2L:12010835-12010955 3.22e-03 41_[+5(9.01e-06)]_71 chr2L:2200329-2200449 3.82e-03 25_[+3(9.76e-06)]_87 chr2R:6158012-6158132 5.93e-02 58_[+1(7.60e-05)]_54 chr2L:18327253-18327373 8.92e-04 3_[+2(2.20e-05)]_[+1(7.60e-05)]_101 chr3L:18771859-18771979 1.13e-02 59_[+3(9.76e-06)]_53 chr2R:24942814-24942934 4.54e-02 111_[+2(2.20e-05)]_1 chrX:17830441-17830561 1.00e+00 120 chr2L:2162212-2162332 9.99e-01 120 chrX:2136469-2136589 3.03e-01 120 chr2R:18351714-18351834 1.87e-01 98_[+2(3.70e-05)]_14 chr2L:16533985-16534105 9.08e-01 120 chrX:20507829-20507949 2.91e-01 120 chr3R:25490487-25490607 1.11e-01 120 chr3L:6189697-6189817 3.50e-01 120 chr3R:5685713-5685833 4.27e-01 120 chr2R:19451177-19451297 1.42e-01 91_[+1(1.09e-05)]_21 chr2L:4218967-4219087 9.99e-01 120 chr2L:8541647-8541767 5.00e-02 120 chrX:21280909-21281029 9.81e-01 120 chr2L:11807169-11807289 6.67e-03 33_[+5(1.29e-05)]_79 chr2L:10221081-10221201 6.12e-01 120 chr2L:11229590-11229710 6.55e-01 120 chr3R:26980485-26980605 4.05e-02 120 chr3R:25050751-25050871 5.86e-01 120 chr2L:14021771-14021891 1.38e-02 120 chr3R:26888447-26888567 9.73e-01 120 chr3L:3852991-3853111 7.81e-01 120 chr3L:4254307-4254427 8.97e-01 120 chr3R:14738871-14738991 9.98e-01 120 chr2R:18834759-18834879 7.02e-01 120 chr3R:16099850-16099970 7.77e-04 37_[+2(5.36e-05)]_4_[+1(6.03e-05)]_\ 63 chr2R:7246859-7246979 3.41e-03 20_[+4(3.41e-05)]_92 chr3R:5659259-5659379 5.10e-01 120 chr3L:11533986-11534106 6.84e-01 120 chr3R:26099383-26099503 8.60e-01 120 chr2L:11209046-11209166 9.94e-01 120 chr3L:1794556-1794676 6.74e-01 120 chrX:11137002-11137122 3.68e-03 77_[+4(4.42e-05)]_35 chr3L:17644419-17644539 5.82e-01 120 chr2L:429816-429936 7.98e-01 120 chr3L:246694-246814 9.00e-01 120 chr3L:10737138-10737258 5.94e-06 43_[+2(1.08e-05)]_15_[+3(9.76e-06)]_\ 13_[+2(6.95e-05)]_25 chr3R:28599653-28599773 6.73e-01 120 chr3R:15093226-15093346 1.00e+00 120 chr2R:8572694-8572814 7.01e-01 120 chrX:12665260-12665380 8.07e-04 13_[+3(2.43e-05)]_18_[+4(3.41e-05)]_\ 73 chr3L:12468165-12468285 1.36e-06 [+2(1.08e-05)]_3_[+3(1.71e-05)]_27_\ [+1(1.09e-05)]_66 chr3R:17053957-17054077 6.10e-02 120 chr3L:626806-626926 1.36e-03 8_[+1(1.09e-05)]_104 chr3R:9352880-9353000 4.60e-01 120 chrX:3862425-3862545 4.22e-01 120 chr2L:15248772-15248892 6.28e-01 120 chr2L:15913434-15913554 2.43e-03 4_[+1(1.09e-05)]_108 chr2L:18944690-18944810 6.74e-01 120 chr2L:11192825-11192945 9.76e-01 120 chr3L:20395337-20395457 5.31e-02 67_[+4(1.74e-05)]_45 chr3L:7867426-7867546 2.88e-02 53_[+2(1.08e-05)]_59 chr2L:11971011-11971131 5.40e-01 120 chr3R:16250115-16250235 1.97e-02 99_[+2(1.08e-05)]_13 chr3R:16748692-16748812 3.66e-02 55_[+4(6.14e-05)]_57 chr3L:18759316-18759436 1.20e-02 24_[+1(5.21e-05)]_88 chr2R:6878494-6878614 6.49e-01 120 chr3R:27245260-27245380 1.64e-05 [+3(9.76e-06)]_32_[+5(9.01e-06)]_32_\ [+4(1.74e-05)]_32 chr2L:7641768-7641888 1.69e-01 120 chr3R:26536330-26536450 1.58e-01 120 chrX:3134421-3134541 9.71e-01 120 chr2L:18590797-18590917 1.73e-01 120 chr2R:15848053-15848173 5.13e-01 120 chr3R:29039754-29039874 3.20e-01 120 chr2L:18328901-18329021 9.41e-01 120 chr3L:6264591-6264711 2.81e-01 120 chr2L:14394644-14394764 9.92e-01 120 chr2R:24531505-24531625 1.39e-01 120 chr2L:2162012-2162132 9.96e-01 120 chr2R:23554578-23554698 9.98e-01 120 chr3L:6816300-6816420 4.77e-01 120 chr2R:13584561-13584681 3.72e-02 120 chr2L:1428372-1428492 6.68e-01 120 chr2R:22174675-22174795 3.10e-02 [+1(3.76e-05)]_112 chr2L:15751124-15751244 1.21e-01 24_[+4(3.41e-05)]_88 chr3R:5060974-5061094 4.08e-01 120 chr4:696780-696900 9.37e-01 120 chr3L:3665423-3665543 9.84e-01 120 chr2R:11275890-11276010 9.85e-01 120 chr2L:3776080-3776200 9.67e-01 120 chr2L:11206797-11206917 9.99e-01 120 chr2R:23383394-23383514 1.21e-03 39_[+3(2.43e-05)]_73 chrX:12469798-12469918 5.87e-01 120 chr3R:9226980-9227100 2.81e-02 110_[+2(3.70e-05)]_2 chr2L:2177715-2177835 8.04e-01 120 chr3L:4239590-4239710 4.42e-01 120 chrX:5517016-5517136 4.76e-02 104_[+2(1.08e-05)]_8 chr3L:628223-628343 5.68e-01 120 chr3R:26052676-26052796 7.50e-01 120 chr2R:24539713-24539833 8.18e-01 120 chr3R:21580173-21580293 4.28e-01 120 chr3R:19118653-19118773 9.38e-01 120 chr2R:14484962-14485082 2.20e-02 67_[+5(9.01e-06)]_45 chr3R:23921370-23921490 9.68e-01 120 chr3R:30601861-30601981 5.22e-01 120 chr2L:13833075-13833195 7.85e-01 120 chr3R:30796877-30796997 3.53e-01 120 chr3L:5185224-5185344 5.46e-04 25_[+4(3.41e-05)]_87 chr3R:14016952-14017072 2.07e-02 54_[+1(3.76e-05)]_58 chr3R:5856485-5856605 3.18e-02 92_[+4(4.42e-05)]_20 chr2L:16887940-16888060 5.75e-01 120 chr2L:12011980-12012100 5.87e-02 120 chrX:2536263-2536383 9.96e-01 120 chrX:14602691-14602811 1.62e-03 89_[+4(3.41e-05)]_23 chrX:3086006-3086126 4.20e-02 92_[+4(1.74e-05)]_20 chr3L:9899152-9899272 7.60e-01 120 chr2R:22686130-22686250 6.75e-02 43_[+2(8.07e-05)]_69 chr2R:12605681-12605801 9.33e-01 120 chr2R:7474282-7474402 9.79e-01 120 chr2L:6088480-6088600 4.32e-03 5_[+2(6.95e-05)]_79_[+2(1.08e-05)]_\ 20 chr2R:24657163-24657283 4.04e-03 91_[+2(2.20e-05)]_6_[+4(1.74e-05)]_\ 7 chr2L:5543183-5543303 9.20e-01 120 chrX:7703000-7703120 4.17e-01 120 chr3L:3070646-3070766 3.23e-03 12_[+2(3.70e-05)]_10_[+1(2.18e-05)]_\ 82 chr2L:161865-161985 1.18e-01 42_[+2(1.08e-05)]_70 chr2R:7492580-7492700 6.98e-01 120 chr2R:24343589-24343709 3.07e-01 120 chr2L:16272886-16273006 4.37e-01 120 chr2R:10475491-10475611 2.80e-02 37_[+5(1.82e-05)]_75 chr3R:29763284-29763404 7.30e-01 120 chrX:14839741-14839861 6.65e-02 70_[+1(1.09e-05)]_42 chr2L:11209251-11209371 1.33e-01 44_[+2(4.51e-05)]_68 chr2L:14094788-14094908 7.66e-01 120 chr3L:7435128-7435248 2.23e-01 120 chr2R:14429845-14429965 3.42e-02 9_[+1(3.76e-05)]_103 chrX:2533966-2534086 3.29e-01 120 chr3R:16241528-16241648 6.81e-04 45_[+1(1.09e-05)]_67 chrX:11454393-11454513 9.63e-01 120 chr3L:17016040-17016160 6.18e-02 120 chr3L:628430-628550 5.29e-02 42_[+5(8.37e-05)]_70 chr3L:17010116-17010236 4.18e-01 120 chr3L:11417277-11417397 1.96e-02 120 chr2R:13584289-13584409 5.59e-01 120 chr3R:14025135-14025255 4.19e-01 120 chr2R:12980580-12980700 1.26e-01 120 chr2R:11600810-11600930 5.94e-01 120 chr3R:17943516-17943636 9.78e-01 120 chr3L:223321-223441 8.15e-01 120 chr2R:18326650-18326770 5.62e-01 120 chr2R:24748944-24749064 9.98e-01 120 chrX:19667022-19667142 1.46e-01 111_[+1(7.60e-05)]_1 chr3R:28887996-28888116 7.48e-01 120 chr2R:7278075-7278195 3.66e-01 120 chr3L:3326257-3326377 7.57e-01 120 chrX:17531967-17532087 5.26e-01 120 chr2L:5256137-5256257 2.34e-01 120 chr3R:29591556-29591676 1.65e-01 120 chrX:6316897-6317017 4.18e-01 120 chr2L:3813427-3813547 1.32e-01 3_[+4(4.42e-05)]_109 chr2L:14122895-14123015 2.35e-02 111_[+4(1.74e-05)]_1 chr3R:14706995-14707115 8.01e-01 120 chrX:13404339-13404459 4.01e-03 64_[+4(3.41e-05)]_48 chr2R:17801031-17801151 1.05e-01 120 chr2L:3872419-3872539 6.09e-02 120 chr3R:10560650-10560770 3.61e-03 120 chrX:19663137-19663257 3.69e-01 120 chr2L:14500591-14500711 9.77e-01 120 chr3L:1740215-1740335 3.65e-01 120 chr2R:11197332-11197452 1.92e-03 67_[+1(1.09e-05)]_45 chr2R:7395959-7396079 7.42e-02 16_[+1(5.21e-05)]_96 chr3R:14473713-14473833 6.34e-01 120 chr2L:2197132-2197252 5.76e-05 17_[+1(1.09e-05)]_75_[+2(1.08e-05)]_\ 12 chr3L:14982732-14982852 6.88e-01 120 chr2L:11269059-11269179 7.22e-01 120 chr3R:24962589-24962709 3.08e-01 120 chr3R:15793474-15793594 7.49e-01 120 chr3R:19644410-19644530 3.85e-01 120 chrX:7703759-7703879 9.92e-01 120 chr3R:29122905-29123025 4.12e-01 120 chr2L:7333247-7333367 1.00e+00 120 chr3R:8305366-8305486 1.73e-01 120 chr3R:8212711-8212831 2.50e-01 68_[+1(2.18e-05)]_44 chr3R:9630740-9630860 9.38e-01 120 chr3R:24169549-24169669 7.10e-01 120 chr2R:18292624-18292744 9.86e-01 120 chr3R:21188817-21188937 1.28e-01 120 chr2L:11498946-11499066 2.59e-01 120 chr3L:10856601-10856721 4.44e-03 49_[+2(3.70e-05)]_[+2(1.08e-05)]_\ [+2(3.70e-05)]_[+2(3.70e-05)]_39 chr2L:14372486-14372606 7.49e-01 120 chr3R:27677350-27677470 5.70e-01 120 chr2L:3303188-3303308 4.08e-04 15_[+3(1.71e-05)]_74_[+2(3.70e-05)]_\ 15 chr2R:19621889-19622009 3.35e-02 1_[+1(1.09e-05)]_111 chr3R:31381403-31381523 9.99e-01 120 chr2R:19452415-19452535 1.19e-01 120 chr3L:10737337-10737457 8.60e-03 94_[+3(9.76e-06)]_18 chr3R:21017608-21017728 2.86e-01 120 chr3R:21487901-21488021 4.42e-01 120 chr3R:10684435-10684555 5.93e-01 120 chr3R:21614991-21615111 2.13e-01 53_[+1(5.21e-05)]_59 chr3L:1479434-1479554 9.03e-01 120 chr2L:14995708-14995828 2.14e-02 83_[+2(3.70e-05)]_29 chr2L:16816430-16816550 2.73e-01 [+4(4.42e-05)]_112 chr3L:13862543-13862663 1.79e-01 120 chr3R:13381983-13382103 1.29e-02 67_[+5(9.01e-06)]_45 chrX:2070781-2070901 9.68e-01 120 chr3R:4659748-4659868 4.95e-02 120 chr2R:5974472-5974592 9.46e-01 120 chr3R:17401419-17401539 2.31e-01 120 chr2L:846295-846415 7.63e-01 120 chr3R:5061174-5061294 5.44e-01 120 chr2R:13579788-13579908 2.84e-01 120 chr2L:2878969-2879089 9.67e-01 120 chr3R:16869353-16869473 4.15e-03 73_[+1(2.18e-05)]_39 chr3R:27282477-27282597 4.39e-02 120 chr2R:10874718-10874838 1.28e-01 92_[+3(8.73e-05)]_20 chr2R:19205430-19205550 1.71e-01 89_[+5(8.37e-05)]_23 chrX:13383867-13383987 3.64e-01 120 chr2R:17872000-17872120 3.56e-01 120 chr2R:23377025-23377145 3.35e-01 120 chr3L:12091464-12091584 5.31e-01 120 chr3R:4378943-4379063 4.93e-02 120 chr2R:20623419-20623539 2.13e-01 120 chr2L:1634146-1634266 3.10e-01 120 chrX:2083263-2083383 1.19e-01 2_[+1(5.21e-05)]_110 chr3R:9598264-9598384 8.02e-01 120 chr2R:16338545-16338665 3.44e-01 120 chr3R:5862358-5862478 2.10e-01 120 chrX:18405855-18405975 9.86e-01 120 chrX:1879689-1879809 8.04e-01 120 chr3L:8153363-8153483 2.08e-02 93_[+4(1.74e-05)]_19 chr3R:9881548-9881668 3.60e-02 48_[+3(4.65e-05)]_38_[+3(9.76e-06)]_\ 18 chr3L:9023693-9023813 6.49e-01 120 chr3L:21539454-21539574 9.02e-01 120 chrX:2270742-2270862 7.40e-01 120 chr3R:11210119-11210239 2.97e-01 120 chr3R:4989689-4989809 7.84e-01 120 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (5) found. ******************************************************************************** CPU: c27n09.farnam.hpc.yale.internal ********************************************************************************