******************************************************************************** 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/CG9948.fasta CONTROL SEQUENCES= --none-- ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ chr3R:5112564-5112684 1.0000 120 chrX:3045547-3045667 1.0000 120 chr2R:14076232-14076352 1.0000 120 chrX:18800334-18800454 1.0000 120 chr3R:5053008-5053128 1.0000 120 chr3L:15187930-15188050 1.0000 120 chr3L:14462479-14462599 1.0000 120 chr2L:15909441-15909561 1.0000 120 chr3L:18245861-18245981 1.0000 120 chr3L:17579194-17579314 1.0000 120 chr3R:13875623-13875743 1.0000 120 chr2R:11083845-11083965 1.0000 120 chr3L:21122625-21122745 1.0000 120 chr3L:16362277-16362397 1.0000 120 chr3L:14145712-14145832 1.0000 120 chr3R:19282980-19283100 1.0000 120 chr3L:17577059-17577179 1.0000 120 chr2R:8995118-8995238 1.0000 120 chr2R:17499278-17499398 1.0000 120 chrX:10202734-10202854 1.0000 120 chr3L:8822359-8822479 1.0000 120 chr3R:29279698-29279818 1.0000 120 chr3R:5389592-5389712 1.0000 120 chr2R:19987206-19987326 1.0000 120 chr3R:29091704-29091824 1.0000 120 chr3L:13215007-13215127 1.0000 120 chrX:6745683-6745803 1.0000 120 chr3L:16747110-16747230 1.0000 120 chr2R:17831922-17832042 1.0000 120 chr3L:6355159-6355279 1.0000 120 chr3R:29072959-29073079 1.0000 120 chr3R:20256749-20256869 1.0000 120 chrX:15123527-15123647 1.0000 120 chr3L:10757102-10757222 1.0000 120 chr3L:15229595-15229715 1.0000 120 chr3R:13848380-13848500 1.0000 120 chrX:17355866-17355986 1.0000 120 chr3L:6391496-6391616 1.0000 120 chr3R:27197770-27197890 1.0000 120 chr2L:1455699-1455819 1.0000 120 chr3R:30265012-30265132 1.0000 120 chr3L:16174894-16175014 1.0000 120 chr3L:18231532-18231652 1.0000 120 chr3L:18191383-18191503 1.0000 120 chr3R:7025384-7025504 1.0000 120 chr3L:8860061-8860181 1.0000 120 chr3L:20914501-20914621 1.0000 120 chr2L:21006690-21006810 1.0000 120 chr2R:17496959-17497079 1.0000 120 chr2L:5288332-5288452 1.0000 120 chr2R:8317636-8317756 1.0000 120 chr2L:13071455-13071575 1.0000 120 chr3L:1421123-1421243 1.0000 120 chr2R:18215417-18215537 1.0000 120 chr2R:18196271-18196391 1.0000 120 chr2L:5479299-5479419 1.0000 120 chr3L:12703580-12703700 1.0000 120 chr3R:10471881-10472001 1.0000 120 chr3R:24970830-24970950 1.0000 120 chrX:11658594-11658714 1.0000 120 chr3L:18078720-18078840 1.0000 120 chr3L:21602373-21602493 1.0000 120 chr3L:20592716-20592836 1.0000 120 chr2L:13146400-13146520 1.0000 120 chr2R:21799424-21799544 1.0000 120 chr2R:15063764-15063884 1.0000 120 chr3L:6799659-6799779 1.0000 120 chrX:5038573-5038693 1.0000 120 chr3L:16259677-16259797 1.0000 120 chr3R:19079275-19079395 1.0000 120 chr2L:16590864-16590984 1.0000 120 chr3R:24953315-24953435 1.0000 120 chr3L:16643133-16643253 1.0000 120 chr2L:1603967-1604087 1.0000 120 chr2L:7868751-7868871 1.0000 120 chr3R:10533289-10533409 1.0000 120 chr3L:12099770-12099890 1.0000 120 chr2R:21377323-21377443 1.0000 120 chr3L:484996-485116 1.0000 120 chr3R:10829919-10830039 1.0000 120 chrX:5020145-5020265 1.0000 120 chr3L:18219477-18219597 1.0000 120 chr3L:21918757-21918877 1.0000 120 chr3L:4749298-4749418 1.0000 120 chr2L:646668-646788 1.0000 120 chr2L:18468136-18468256 1.0000 120 chr2R:13473963-13474083 1.0000 120 chr2R:16715480-16715600 1.0000 120 chrX:17829783-17829903 1.0000 120 chr2L:21005577-21005697 1.0000 120 chr3L:10386319-10386439 1.0000 120 chr3L:10923113-10923233 1.0000 120 chr2R:21854570-21854690 1.0000 120 chr3L:14350947-14351067 1.0000 120 chr3R:8958450-8958570 1.0000 120 chr2L:15364180-15364300 1.0000 120 chr2L:14569421-14569541 1.0000 120 chr3L:10904895-10905015 1.0000 120 chrX:9654094-9654214 1.0000 120 chrX:13345420-13345540 1.0000 120 chrX:18929571-18929691 1.0000 120 chr3R:24024263-24024383 1.0000 120 chrX:18540394-18540514 1.0000 120 chr2L:4028102-4028222 1.0000 120 chr3L:21253075-21253195 1.0000 120 chr3L:15005866-15005986 1.0000 120 chr3R:29280800-29280920 1.0000 120 chr3L:13173101-13173221 1.0000 120 chr3R:21649602-21649722 1.0000 120 chr2L:13268390-13268510 1.0000 120 chr3R:22158412-22158532 1.0000 120 chr3L:18244357-18244477 1.0000 120 chr3L:4691857-4691977 1.0000 120 chr3L:16972185-16972305 1.0000 120 chrX:17807091-17807211 1.0000 120 chr3L:15013433-15013553 1.0000 120 chr2L:20002180-20002300 1.0000 120 chr2R:15000550-15000670 1.0000 120 chr3R:30259696-30259816 1.0000 120 chr3L:5128383-5128503 1.0000 120 chr2R:19968852-19968972 1.0000 120 chr3R:26019319-26019439 1.0000 120 chr2L:11069670-11069790 1.0000 120 chr3L:20582507-20582627 1.0000 120 chr2R:9071846-9071966 1.0000 120 chr3L:6084616-6084736 1.0000 120 chr3R:13916708-13916828 1.0000 120 chr2L:1459489-1459609 1.0000 120 chr3L:14353287-14353407 1.0000 120 chrX:379652-379772 1.0000 120 chrX:8215603-8215723 1.0000 120 chr3L:3072129-3072249 1.0000 120 chr2L:2432970-2433090 1.0000 120 chrX:14922559-14922679 1.0000 120 chr3L:6458839-6458959 1.0000 120 chr2L:17421542-17421662 1.0000 120 chrX:8839506-8839626 1.0000 120 chr2R:14929635-14929755 1.0000 120 chr3R:22184192-22184312 1.0000 120 chrX:7540911-7541031 1.0000 120 chr3L:15180957-15181077 1.0000 120 chr3L:767068-767188 1.0000 120 chr3L:3444401-3444521 1.0000 120 chr3L:3513147-3513267 1.0000 120 chr2L:19156611-19156731 1.0000 120 chr3L:13178377-13178497 1.0000 120 chr2R:19149871-19149991 1.0000 120 chr3L:20990376-20990496 1.0000 120 chr2R:15825536-15825656 1.0000 120 chr3L:16489903-16490023 1.0000 120 chr2R:6521264-6521384 1.0000 120 chrX:15639158-15639278 1.0000 120 chr3R:7953121-7953241 1.0000 120 chr2R:18907112-18907232 1.0000 120 chr3R:26832017-26832137 1.0000 120 chr3R:29570399-29570519 1.0000 120 chr3R:14421921-14422041 1.0000 120 chrX:21073780-21073900 1.0000 120 chr2R:18343073-18343193 1.0000 120 chr3L:17926632-17926752 1.0000 120 chrX:17537405-17537525 1.0000 120 chr2R:8318281-8318401 1.0000 120 chrX:7558785-7558905 1.0000 120 chr3L:11373998-11374118 1.0000 120 chr2R:21550613-21550733 1.0000 120 chr2L:15390591-15390711 1.0000 120 chr3L:9209150-9209270 1.0000 120 chr3R:8922961-8923081 1.0000 120 chr2L:3582826-3582946 1.0000 120 chr2R:6134018-6134138 1.0000 120 chr3L:13109438-13109558 1.0000 120 chr2L:3562487-3562607 1.0000 120 chr3R:31944357-31944477 1.0000 120 chr2L:15386853-15386973 1.0000 120 chr3R:18998481-18998601 1.0000 120 chr3L:18079657-18079777 1.0000 120 chr3L:4731815-4731935 1.0000 120 chr3R:14373958-14374078 1.0000 120 chr2R:11749563-11749683 1.0000 120 chr2L:14236256-14236376 1.0000 120 chr3R:14691625-14691745 1.0000 120 chr3L:14422236-14422356 1.0000 120 chr2L:4069606-4069726 1.0000 120 chr3L:21720982-21721102 1.0000 120 chrX:14134059-14134179 1.0000 120 chr3L:6371543-6371663 1.0000 120 chr3R:21653097-21653217 1.0000 120 chr3L:15240874-15240994 1.0000 120 chr2L:5372697-5372817 1.0000 120 chr2R:14317124-14317244 1.0000 120 chr3R:29290998-29291118 1.0000 120 chr3R:27179107-27179227 1.0000 120 chr3R:30171526-30171646 1.0000 120 chr3R:23878433-23878553 1.0000 120 chr2L:18005611-18005731 1.0000 120 chr3R:8811009-8811129 1.0000 120 chr2R:24807834-24807954 1.0000 120 chr3R:14292507-14292627 1.0000 120 chr2L:7971525-7971645 1.0000 120 chr3L:13212989-13213109 1.0000 120 chr2R:21847838-21847958 1.0000 120 chr3R:7651156-7651276 1.0000 120 chr3L:15264793-15264913 1.0000 120 chr2L:16281818-16281938 1.0000 120 chr2L:18482253-18482373 1.0000 120 chr3L:14350293-14350413 1.0000 120 chr3L:18243393-18243513 1.0000 120 chr3L:7994022-7994142 1.0000 120 chr3L:20635691-20635811 1.0000 120 chr3L:2830128-2830248 1.0000 120 chr3L:6446705-6446825 1.0000 120 chr2R:11452578-11452698 1.0000 120 chr3R:18469585-18469705 1.0000 120 chr3R:7646330-7646450 1.0000 120 chrX:21127408-21127528 1.0000 120 chr3R:24261749-24261869 1.0000 120 chr2R:14082359-14082479 1.0000 120 chr2L:7899281-7899401 1.0000 120 chr3L:14610640-14610760 1.0000 120 chr3R:14673065-14673185 1.0000 120 chr2L:11052517-11052637 1.0000 120 chr3R:30256371-30256491 1.0000 120 chr3R:13846011-13846131 1.0000 120 chr3L:3074483-3074603 1.0000 120 chr3R:17202439-17202559 1.0000 120 chr3L:15174279-15174399 1.0000 120 chr2L:16594028-16594148 1.0000 120 chr3L:8765609-8765729 1.0000 120 chr3L:5633715-5633835 1.0000 120 chr2L:15459036-15459156 1.0000 120 chr3L:6458019-6458139 1.0000 120 chr3L:10928849-10928969 1.0000 120 chr2R:23306104-23306224 1.0000 120 chr3L:14239451-14239571 1.0000 120 chr2R:12535193-12535313 1.0000 120 chrX:6022217-6022337 1.0000 120 chr2L:18122271-18122391 1.0000 120 chr3L:9567003-9567123 1.0000 120 chr2L:1456964-1457084 1.0000 120 chr3R:16210801-16210921 1.0000 120 chr3R:14390576-14390696 1.0000 120 chrX:4442619-4442739 1.0000 120 chr3L:14146506-14146626 1.0000 120 chr3L:8881884-8882004 1.0000 120 chr2R:18566111-18566231 1.0000 120 chr2L:5751575-5751695 1.0000 120 chr3R:11154013-11154133 1.0000 120 chr2L:20721592-20721712 1.0000 120 chr3R:4687336-4687456 1.0000 120 chr3L:13107428-13107548 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_CG9948/ -dna -nmotifs 5 -w 8 -maxsize 250000 -nostatus ../result/final_prediction/fly/fasta/RankLinear8.0_60/CG9948.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 0.369 C 0.133 G 0.136 T 0.362 Background letter frequencies (from file dataset with add-one prior applied): A 0.369 C 0.133 G 0.136 T 0.362 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF GGCSCCAC MEME-1 width = 8 sites = 2 llr = 29 E-value = 3.1e+003 ******************************************************************************** -------------------------------------------------------------------------------- Motif GGCSCCAC MEME-1 Description -------------------------------------------------------------------------------- Simplified A ::::::a: pos.-specific C ::a5aa:a probability G aa:5:::: matrix T :::::::: bits 2.9 *** ** * 2.6 *** ** * 2.3 *** ** * 2.0 ****** * Relative 1.7 ****** * Entropy 1.5 ******** (20.7 bits) 1.2 ******** 0.9 ******** 0.6 ******** 0.3 ******** 0.0 -------- Multilevel GGCCCCAC consensus G sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGCSCCAC MEME-1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr2L:3562487-3562607 47 2.84e-07 TTATGTACTT GGCCCCAC GTTGGGCGCT chr2R:11083845-11083965 78 5.74e-07 TCTTGCTAAA GGCGCCAC GTAAAACTTT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGCSCCAC MEME-1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr2L:3562487-3562607 2.8e-07 46_[+1]_66 chr2R:11083845-11083965 5.7e-07 77_[+1]_35 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGCSCCAC MEME-1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF GGCSCCAC width=8 seqs=2 chr2L:3562487-3562607 ( 47) GGCCCCAC 1 chr2R:11083845-11083965 ( 78) GGCGCCAC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGCSCCAC MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 28250 bayes= 12.9378 E= 3.1e+003 -765 -765 288 -765 -765 -765 288 -765 -765 290 -765 -765 -765 190 188 -765 -765 290 -765 -765 -765 290 -765 -765 143 -765 -765 -765 -765 290 -765 -765 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGCSCCAC MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 2 E= 3.1e+003 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 0.500000 0.500000 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 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGCSCCAC MEME-1 regular expression -------------------------------------------------------------------------------- GGC[CG]CCAC -------------------------------------------------------------------------------- Time 7.43 secs. ******************************************************************************** ******************************************************************************** MOTIF CAGCCCMC MEME-2 width = 8 sites = 2 llr = 28 E-value = 8.6e+003 ******************************************************************************** -------------------------------------------------------------------------------- Motif CAGCCCMC MEME-2 Description -------------------------------------------------------------------------------- Simplified A :a::::5: pos.-specific C a::aaa5a probability G ::a::::: matrix T :::::::: bits 2.9 * **** * 2.6 * **** * 2.3 * **** * 2.0 * **** * Relative 1.7 * **** * Entropy 1.5 ****** * (20.0 bits) 1.2 ******** 0.9 ******** 0.6 ******** 0.3 ******** 0.0 -------- Multilevel CAGCCCAC consensus C sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CAGCCCMC MEME-2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr3R:30265012-30265132 19 2.78e-07 ATCAACGCGT CAGCCCCC TTACACTGGA chr3R:29072959-29073079 28 1.05e-06 TAGTTTCAAA CAGCCCAC ATATAACCTT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CAGCCCMC MEME-2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr3R:30265012-30265132 2.8e-07 18_[+2]_94 chr3R:29072959-29073079 1e-06 27_[+2]_85 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CAGCCCMC MEME-2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF CAGCCCMC width=8 seqs=2 chr3R:30265012-30265132 ( 19) CAGCCCCC 1 chr3R:29072959-29073079 ( 28) CAGCCCAC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CAGCCCMC MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 28250 bayes= 12.9378 E= 8.6e+003 -765 290 -765 -765 143 -765 -765 -765 -765 -765 288 -765 -765 290 -765 -765 -765 290 -765 -765 -765 290 -765 -765 44 190 -765 -765 -765 290 -765 -765 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CAGCCCMC MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 2 E= 8.6e+003 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 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.500000 0.500000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CAGCCCMC MEME-2 regular expression -------------------------------------------------------------------------------- CAGCCC[AC]C -------------------------------------------------------------------------------- Time 13.62 secs. ******************************************************************************** ******************************************************************************** MOTIF ACCCCCTS MEME-3 width = 8 sites = 2 llr = 27 E-value = 7.0e+003 ******************************************************************************** -------------------------------------------------------------------------------- Motif ACCCCCTS MEME-3 Description -------------------------------------------------------------------------------- Simplified A a::::::: pos.-specific C :aaaaa:5 probability G :::::::5 matrix T ::::::a: bits 2.9 ***** 2.6 ***** 2.3 ***** 2.0 ***** * Relative 1.7 ***** * Entropy 1.5 ******** (19.3 bits) 1.2 ******** 0.9 ******** 0.6 ******** 0.3 ******** 0.0 -------- Multilevel ACCCCCTC consensus G sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ACCCCCTS MEME-3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr2R:23306104-23306224 87 7.39e-07 AATCATCAAA ACCCCCTC CATTTCTGGG chr2R:9071846-9071966 91 1.50e-06 CTAAAGTGCT ACCCCCTG TACCCCCACA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ACCCCCTS MEME-3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr2R:23306104-23306224 7.4e-07 86_[+3]_26 chr2R:9071846-9071966 1.5e-06 90_[+3]_22 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ACCCCCTS MEME-3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF ACCCCCTS width=8 seqs=2 chr2R:23306104-23306224 ( 87) ACCCCCTC 1 chr2R:9071846-9071966 ( 91) ACCCCCTG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ACCCCCTS MEME-3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 28250 bayes= 13.7859 E= 7.0e+003 143 -765 -765 -765 -765 290 -765 -765 -765 290 -765 -765 -765 290 -765 -765 -765 290 -765 -765 -765 290 -765 -765 -765 -765 -765 146 -765 190 188 -765 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ACCCCCTS MEME-3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 2 E= 7.0e+003 1.000000 0.000000 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 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.500000 0.500000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ACCCCCTS MEME-3 regular expression -------------------------------------------------------------------------------- ACCCCCT[CG] -------------------------------------------------------------------------------- Time 19.87 secs. ******************************************************************************** ******************************************************************************** MOTIF ACTGAGMG MEME-4 width = 8 sites = 11 llr = 116 E-value = 1.7e+004 ******************************************************************************** -------------------------------------------------------------------------------- Motif ACTGAGMG MEME-4 Description -------------------------------------------------------------------------------- Simplified A a:2:9:6: pos.-specific C :a::::42 probability G :::a1a:8 matrix T ::8::::: bits 2.9 * * * 2.6 * * * 2.3 * * * * 2.0 * * * * Relative 1.7 * * * * Entropy 1.5 ** * * * (15.2 bits) 1.2 ** ***** 0.9 ******** 0.6 ******** 0.3 ******** 0.0 -------- Multilevel ACTGAGAG consensus C sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ACTGAGMG MEME-4 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr3L:8765609-8765729 72 2.19e-06 TTACCTTTTT ACTGAGCG CTTTATTTTA chr3L:6446705-6446825 6 8.28e-06 AAAAA ACTGAGAG AAAATTGATT chr3L:15264793-15264913 74 8.28e-06 CTATATTTAG ACTGAGAG AAGTGTTTTA chr3R:14421921-14422041 18 8.28e-06 TCAGAACCAC ACTGAGAG AAAATCTTTT chr3L:10904895-10905015 2 8.28e-06 C ACTGAGAG AAAAGTAGTG chr3L:18219477-18219597 10 8.28e-06 TGCCAGATC ACTGAGAG AAAACAGGGT chr2R:19149871-19149991 6 1.35e-05 GAGGC ACTGAGCC AAAAAGCCAA chrX:6745683-6745803 4 1.35e-05 TGC ACAGAGCG AAAATGTGGC chrX:3045547-3045667 72 1.35e-05 TATATATTAA ACTGAGCC AGATATACAA chr3R:21653097-21653217 3 1.57e-05 AT ACTGGGAG AGATGGTCTT chr2R:14076232-14076352 104 2.79e-05 ATTAAACGAA ACAGAGAG CAAAGCTCT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ACTGAGMG MEME-4 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr3L:8765609-8765729 2.2e-06 71_[+4]_41 chr3L:6446705-6446825 8.3e-06 5_[+4]_107 chr3L:15264793-15264913 8.3e-06 73_[+4]_39 chr3R:14421921-14422041 8.3e-06 17_[+4]_95 chr3L:10904895-10905015 8.3e-06 1_[+4]_111 chr3L:18219477-18219597 8.3e-06 9_[+4]_103 chr2R:19149871-19149991 1.3e-05 5_[+4]_107 chrX:6745683-6745803 1.3e-05 3_[+4]_109 chrX:3045547-3045667 1.3e-05 71_[+4]_41 chr3R:21653097-21653217 1.6e-05 2_[+4]_110 chr2R:14076232-14076352 2.8e-05 103_[+4]_9 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ACTGAGMG MEME-4 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF ACTGAGMG width=8 seqs=11 chr3L:8765609-8765729 ( 72) ACTGAGCG 1 chr3L:6446705-6446825 ( 6) ACTGAGAG 1 chr3L:15264793-15264913 ( 74) ACTGAGAG 1 chr3R:14421921-14422041 ( 18) ACTGAGAG 1 chr3L:10904895-10905015 ( 2) ACTGAGAG 1 chr3L:18219477-18219597 ( 10) ACTGAGAG 1 chr2R:19149871-19149991 ( 6) ACTGAGCC 1 chrX:6745683-6745803 ( 4) ACAGAGCG 1 chrX:3045547-3045667 ( 72) ACTGAGCC 1 chr3R:21653097-21653217 ( 3) ACTGGGAG 1 chr2R:14076232-14076352 ( 104) ACAGAGAG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ACTGAGMG MEME-4 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 28250 bayes= 10.8783 E= 1.7e+004 144 -1010 -1010 -1010 -1010 291 -1010 -1010 -102 -1010 -1010 118 -1010 -1010 288 -1010 130 -1010 -58 -1010 -1010 -1010 288 -1010 78 145 -1010 -1010 -1010 45 259 -1010 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ACTGAGMG MEME-4 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 11 E= 1.7e+004 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.181818 0.000000 0.000000 0.818182 0.000000 0.000000 1.000000 0.000000 0.909091 0.000000 0.090909 0.000000 0.000000 0.000000 1.000000 0.000000 0.636364 0.363636 0.000000 0.000000 0.000000 0.181818 0.818182 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ACTGAGMG MEME-4 regular expression -------------------------------------------------------------------------------- ACTGAG[AC]G -------------------------------------------------------------------------------- Time 26.03 secs. ******************************************************************************** ******************************************************************************** MOTIF SCCGCMCA MEME-5 width = 8 sites = 2 llr = 26 E-value = 2.4e+004 ******************************************************************************** -------------------------------------------------------------------------------- Motif SCCGCMCA MEME-5 Description -------------------------------------------------------------------------------- Simplified A :::::5:a pos.-specific C 5aa:a5a: probability G 5::a:::: matrix T :::::::: bits 2.9 **** * 2.6 **** * 2.3 **** * 2.0 ***** * Relative 1.7 ***** * Entropy 1.5 ***** ** (19.0 bits) 1.2 ******** 0.9 ******** 0.6 ******** 0.3 ******** 0.0 -------- Multilevel CCCGCACA consensus G C sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif SCCGCMCA MEME-5 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr3R:29091704-29091824 18 5.62e-07 AACAATTGAT GCCGCCCA TTAAATTATT chr3L:8822359-8822479 69 1.33e-06 CTCCAAAATT CCCGCACA GTTTAAGAAA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif SCCGCMCA MEME-5 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr3R:29091704-29091824 5.6e-07 17_[+5]_95 chr3L:8822359-8822479 1.3e-06 68_[+5]_44 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif SCCGCMCA MEME-5 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF SCCGCMCA width=8 seqs=2 chr3R:29091704-29091824 ( 18) GCCGCCCA 1 chr3L:8822359-8822479 ( 69) CCCGCACA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif SCCGCMCA MEME-5 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 28250 bayes= 13.7859 E= 2.4e+004 -765 190 188 -765 -765 290 -765 -765 -765 290 -765 -765 -765 -765 288 -765 -765 290 -765 -765 44 190 -765 -765 -765 290 -765 -765 143 -765 -765 -765 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif SCCGCMCA MEME-5 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 2 E= 2.4e+004 0.000000 0.500000 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 0.500000 0.500000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif SCCGCMCA MEME-5 regular expression -------------------------------------------------------------------------------- [CG]CCGC[AC]CA -------------------------------------------------------------------------------- Time 32.21 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr3R:5112564-5112684 2.56e-01 120 chrX:3045547-3045667 2.74e-02 71_[+4(1.35e-05)]_41 chr2R:14076232-14076352 2.62e-02 103_[+4(2.79e-05)]_9 chrX:18800334-18800454 7.73e-01 120 chr3R:5053008-5053128 2.78e-02 26_[+5(9.43e-05)]_86 chr3L:15187930-15188050 9.96e-01 120 chr3L:14462479-14462599 9.81e-01 120 chr2L:15909441-15909561 6.54e-01 120 chr3L:18245861-18245981 9.92e-01 120 chr3L:17579194-17579314 8.33e-02 120 chr3R:13875623-13875743 9.83e-01 120 chr2R:11083845-11083965 4.78e-03 77_[+1(5.74e-07)]_35 chr3L:21122625-21122745 1.00e+00 120 chr3L:16362277-16362397 1.00e+00 120 chr3L:14145712-14145832 9.44e-01 120 chr3R:19282980-19283100 1.89e-01 120 chr3L:17577059-17577179 3.97e-01 120 chr2R:8995118-8995238 5.65e-01 120 chr2R:17499278-17499398 9.95e-01 120 chrX:10202734-10202854 6.27e-01 120 chr3L:8822359-8822479 3.25e-04 68_[+5(1.33e-06)]_44 chr3R:29279698-29279818 6.69e-01 120 chr3R:5389592-5389712 7.11e-01 120 chr2R:19987206-19987326 9.91e-01 120 chr3R:29091704-29091824 8.12e-06 17_[+5(5.62e-07)]_58_[+3(5.95e-05)]_\ 29 chr3L:13215007-13215127 6.94e-01 120 chrX:6745683-6745803 3.64e-03 3_[+4(1.35e-05)]_109 chr3L:16747110-16747230 1.00e+00 120 chr2R:17831922-17832042 7.99e-01 120 chr3L:6355159-6355279 8.81e-01 120 chr3R:29072959-29073079 1.21e-03 27_[+2(1.05e-06)]_85 chr3R:20256749-20256869 9.72e-01 120 chrX:15123527-15123647 2.89e-01 120 chr3L:10757102-10757222 9.35e-02 120 chr3L:15229595-15229715 8.02e-01 120 chr3R:13848380-13848500 9.99e-01 120 chrX:17355866-17355986 4.23e-01 120 chr3L:6391496-6391616 2.23e-01 120 chr3R:27197770-27197890 8.81e-02 120 chr2L:1455699-1455819 9.83e-01 120 chr3R:30265012-30265132 1.42e-05 18_[+2(2.78e-07)]_94 chr3L:16174894-16175014 4.56e-01 120 chr3L:18231532-18231652 9.83e-01 120 chr3L:18191383-18191503 9.23e-01 120 chr3R:7025384-7025504 1.26e-01 120 chr3L:8860061-8860181 9.20e-01 120 chr3L:20914501-20914621 3.89e-01 120 chr2L:21006690-21006810 3.20e-01 120 chr2R:17496959-17497079 5.04e-01 120 chr2L:5288332-5288452 5.32e-01 120 chr2R:8317636-8317756 6.26e-01 120 chr2L:13071455-13071575 5.46e-01 120 chr3L:1421123-1421243 9.37e-01 120 chr2R:18215417-18215537 1.00e+00 120 chr2R:18196271-18196391 8.59e-01 120 chr2L:5479299-5479419 2.93e-01 120 chr3L:12703580-12703700 9.97e-01 120 chr3R:10471881-10472001 1.00e+00 120 chr3R:24970830-24970950 2.66e-01 120 chrX:11658594-11658714 1.50e-01 120 chr3L:18078720-18078840 6.37e-01 120 chr3L:21602373-21602493 9.37e-01 120 chr3L:20592716-20592836 3.70e-01 120 chr2L:13146400-13146520 6.19e-01 120 chr2R:21799424-21799544 8.66e-01 120 chr2R:15063764-15063884 4.37e-01 120 chr3L:6799659-6799779 9.07e-02 120 chrX:5038573-5038693 1.92e-01 26_[+5(8.24e-05)]_86 chr3L:16259677-16259797 8.45e-01 120 chr3R:19079275-19079395 8.91e-01 120 chr2L:16590864-16590984 9.44e-01 120 chr3R:24953315-24953435 8.96e-01 120 chr3L:16643133-16643253 6.95e-01 120 chr2L:1603967-1604087 8.86e-01 120 chr2L:7868751-7868871 8.34e-03 71_[+2(4.47e-05)]_41 chr3R:10533289-10533409 5.58e-01 120 chr3L:12099770-12099890 2.41e-01 120 chr2R:21377323-21377443 9.99e-01 120 chr3L:484996-485116 1.26e-01 120 chr3R:10829919-10830039 7.57e-01 120 chrX:5020145-5020265 9.97e-01 120 chr3L:18219477-18219597 9.53e-03 9_[+4(8.28e-06)]_103 chr3L:21918757-21918877 8.68e-01 120 chr3L:4749298-4749418 9.83e-01 120 chr2L:646668-646788 3.91e-01 120 chr2L:18468136-18468256 5.50e-02 111_[+3(7.81e-05)]_1 chr2R:13473963-13474083 8.50e-01 120 chr2R:16715480-16715600 4.19e-01 120 chrX:17829783-17829903 4.27e-01 120 chr2L:21005577-21005697 9.77e-01 120 chr3L:10386319-10386439 9.45e-01 120 chr3L:10923113-10923233 4.30e-01 94_[+4(9.67e-05)]_18 chr2R:21854570-21854690 1.46e-03 30_[+2(4.47e-05)]_82 chr3L:14350947-14351067 2.10e-01 120 chr3R:8958450-8958570 7.70e-01 120 chr2L:15364180-15364300 9.54e-01 120 chr2L:14569421-14569541 1.00e+00 120 chr3L:10904895-10905015 1.02e-01 1_[+4(8.28e-06)]_111 chrX:9654094-9654214 1.00e+00 120 chrX:13345420-13345540 8.08e-01 120 chrX:18929571-18929691 5.62e-01 120 chr3R:24024263-24024383 6.58e-01 120 chrX:18540394-18540514 1.00e+00 120 chr2L:4028102-4028222 9.65e-01 120 chr3L:21253075-21253195 3.55e-01 120 chr3L:15005866-15005986 8.15e-01 120 chr3R:29280800-29280920 8.63e-01 120 chr3L:13173101-13173221 9.99e-01 120 chr3R:21649602-21649722 1.05e-01 120 chr2L:13268390-13268510 8.40e-01 120 chr3R:22158412-22158532 7.37e-01 120 chr3L:18244357-18244477 9.70e-01 120 chr3L:4691857-4691977 1.20e-01 120 chr3L:16972185-16972305 7.79e-01 120 chrX:17807091-17807211 1.00e+00 120 chr3L:15013433-15013553 9.43e-01 120 chr2L:20002180-20002300 9.11e-01 120 chr2R:15000550-15000670 7.06e-01 120 chr3R:30259696-30259816 9.75e-01 120 chr3L:5128383-5128503 7.39e-05 94_[+2(4.65e-05)]_18 chr2R:19968852-19968972 4.88e-01 120 chr3R:26019319-26019439 9.85e-01 120 chr2L:11069670-11069790 9.13e-01 120 chr3L:20582507-20582627 2.29e-02 55_[+1(4.69e-05)]_57 chr2R:9071846-9071966 2.81e-06 90_[+3(1.50e-06)]_1_[+3(4.06e-06)]_\ 13 chr3L:6084616-6084736 2.07e-01 120 chr3R:13916708-13916828 8.78e-01 120 chr2L:1459489-1459609 4.15e-01 120 chr3L:14353287-14353407 9.76e-01 120 chrX:379652-379772 6.69e-01 120 chrX:8215603-8215723 1.00e+00 120 chr3L:3072129-3072249 9.31e-01 120 chr2L:2432970-2433090 9.59e-01 120 chrX:14922559-14922679 4.64e-01 120 chr3L:6458839-6458959 4.51e-01 120 chr2L:17421542-17421662 1.00e+00 120 chrX:8839506-8839626 9.84e-01 120 chr2R:14929635-14929755 1.37e-01 120 chr3R:22184192-22184312 9.59e-01 120 chrX:7540911-7541031 8.31e-01 120 chr3L:15180957-15181077 7.16e-02 120 chr3L:767068-767188 2.54e-01 120 chr3L:3444401-3444521 1.83e-01 120 chr3L:3513147-3513267 5.61e-01 120 chr2L:19156611-19156731 2.91e-01 120 chr3L:13178377-13178497 8.77e-01 120 chr2R:19149871-19149991 1.68e-02 5_[+4(1.35e-05)]_107 chr3L:20990376-20990496 5.32e-01 120 chr2R:15825536-15825656 8.59e-01 120 chr3L:16489903-16490023 6.87e-01 120 chr2R:6521264-6521384 4.85e-01 120 chrX:15639158-15639278 9.98e-01 120 chr3R:7953121-7953241 8.56e-01 120 chr2R:18907112-18907232 9.99e-01 120 chr3R:26832017-26832137 9.34e-01 120 chr3R:29570399-29570519 9.53e-01 120 chr3R:14421921-14422041 4.94e-03 17_[+4(8.28e-06)]_95 chrX:21073780-21073900 7.41e-01 120 chr2R:18343073-18343193 5.46e-01 120 chr3L:17926632-17926752 9.44e-01 120 chrX:17537405-17537525 8.79e-01 120 chr2R:8318281-8318401 1.67e-01 120 chrX:7558785-7558905 9.93e-01 120 chr3L:11373998-11374118 1.00e+00 120 chr2R:21550613-21550733 3.05e-02 112_[+2(6.50e-05)] chr2L:15390591-15390711 9.92e-01 120 chr3L:9209150-9209270 9.97e-01 120 chr3R:8922961-8923081 7.17e-02 120 chr2L:3582826-3582946 1.11e-01 120 chr2R:6134018-6134138 2.54e-01 120 chr3L:13109438-13109558 8.50e-01 120 chr2L:3562487-3562607 2.21e-05 46_[+1(2.84e-07)]_66 chr3R:31944357-31944477 1.58e-01 120 chr2L:15386853-15386973 6.42e-01 120 chr3R:18998481-18998601 2.73e-01 120 chr3L:18079657-18079777 8.40e-01 120 chr3L:4731815-4731935 2.01e-01 120 chr3R:14373958-14374078 4.20e-01 120 chr2R:11749563-11749683 5.88e-01 120 chr2L:14236256-14236376 9.81e-01 120 chr3R:14691625-14691745 1.00e+00 120 chr3L:14422236-14422356 9.98e-01 120 chr2L:4069606-4069726 9.98e-01 120 chr3L:21720982-21721102 8.73e-01 120 chrX:14134059-14134179 8.04e-01 120 chr3L:6371543-6371663 9.86e-01 120 chr3R:21653097-21653217 2.35e-02 2_[+4(1.57e-05)]_110 chr3L:15240874-15240994 2.05e-02 27_[+2(4.47e-05)]_85 chr2L:5372697-5372817 9.18e-01 120 chr2R:14317124-14317244 6.79e-01 120 chr3R:29290998-29291118 8.44e-01 120 chr3R:27179107-27179227 8.18e-01 120 chr3R:30171526-30171646 6.61e-01 120 chr3R:23878433-23878553 8.14e-01 120 chr2L:18005611-18005731 8.58e-01 120 chr3R:8811009-8811129 6.16e-01 120 chr2R:24807834-24807954 2.31e-01 120 chr3R:14292507-14292627 6.18e-01 120 chr2L:7971525-7971645 6.93e-01 120 chr3L:13212989-13213109 5.20e-01 120 chr2R:21847838-21847958 6.48e-01 120 chr3R:7651156-7651276 9.34e-01 120 chr3L:15264793-15264913 1.18e-02 73_[+4(8.28e-06)]_39 chr2L:16281818-16281938 6.48e-01 120 chr2L:18482253-18482373 6.07e-01 120 chr3L:14350293-14350413 4.92e-01 120 chr3L:18243393-18243513 4.83e-02 120 chr3L:7994022-7994142 9.81e-01 120 chr3L:20635691-20635811 3.91e-01 120 chr3L:2830128-2830248 9.78e-01 120 chr3L:6446705-6446825 7.76e-02 5_[+4(8.28e-06)]_107 chr2R:11452578-11452698 1.98e-04 67_[+4(4.30e-05)]_45 chr3R:18469585-18469705 9.73e-01 120 chr3R:7646330-7646450 2.73e-01 120 chrX:21127408-21127528 4.73e-01 120 chr3R:24261749-24261869 2.69e-01 120 chr2R:14082359-14082479 1.00e+00 120 chr2L:7899281-7899401 2.46e-01 120 chr3L:14610640-14610760 9.96e-01 120 chr3R:14673065-14673185 5.21e-01 120 chr2L:11052517-11052637 4.92e-02 120 chr3R:30256371-30256491 9.98e-01 120 chr3R:13846011-13846131 6.91e-01 120 chr3L:3074483-3074603 9.70e-01 120 chr3R:17202439-17202559 9.51e-01 120 chr3L:15174279-15174399 9.45e-01 120 chr2L:16594028-16594148 7.02e-01 120 chr3L:8765609-8765729 1.15e-02 71_[+4(2.19e-06)]_41 chr3L:5633715-5633835 8.82e-01 120 chr2L:15459036-15459156 2.76e-01 120 chr3L:6458019-6458139 6.50e-02 120 chr3L:10928849-10928969 8.33e-01 120 chr2R:23306104-23306224 2.77e-05 86_[+3(7.39e-07)]_26 chr3L:14239451-14239571 8.34e-01 120 chr2R:12535193-12535313 4.98e-01 120 chrX:6022217-6022337 5.29e-01 120 chr2L:18122271-18122391 1.35e-01 120 chr3L:9567003-9567123 9.44e-01 120 chr2L:1456964-1457084 4.23e-04 112_[+1(1.41e-05)] chr3R:16210801-16210921 9.81e-01 120 chr3R:14390576-14390696 4.19e-01 120 chrX:4442619-4442739 4.87e-01 120 chr3L:14146506-14146626 8.56e-01 120 chr3L:8881884-8882004 1.40e-01 120 chr2R:18566111-18566231 9.93e-01 120 chr2L:5751575-5751695 8.47e-01 120 chr3R:11154013-11154133 1.00e+00 120 chr2L:20721592-20721712 3.05e-01 120 chr3R:4687336-4687456 6.26e-01 120 chr3L:13107428-13107548 8.73e-01 120 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (5) found. ******************************************************************************** CPU: c27n06.farnam.hpc.yale.internal ********************************************************************************