******************************************************************************** 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/CG32006.fasta CONTROL SEQUENCES= --none-- ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ chr2R:12603475-12603595 1.0000 120 chr2L:17492793-17492913 1.0000 120 chr3L:5609608-5609728 1.0000 120 chr3R:19808171-19808291 1.0000 120 chr3L:1200474-1200594 1.0000 120 chr2R:16742121-16742241 1.0000 120 chr3L:8422407-8422527 1.0000 120 chr2R:7734085-7734205 1.0000 120 chrX:10953377-10953497 1.0000 120 chr2L:13925806-13925926 1.0000 120 chr3R:8948193-8948313 1.0000 120 chr2R:7905093-7905213 1.0000 120 chr2L:20295995-20296115 1.0000 120 chr3L:19329630-19329750 1.0000 120 chr2R:20024376-20024496 1.0000 120 chr3L:10398821-10398941 1.0000 120 chr2L:19307778-19307898 1.0000 120 chr3R:6215140-6215260 1.0000 120 chr3R:24219238-24219358 1.0000 120 chr2L:15321596-15321716 1.0000 120 chr3R:15922724-15922844 1.0000 120 chr2R:13769489-13769609 1.0000 120 chr2L:14370864-14370984 1.0000 120 chr3L:1905392-1905512 1.0000 120 chr2R:8353392-8353512 1.0000 120 chr2L:11505390-11505510 1.0000 120 chr2R:12413254-12413374 1.0000 120 chr2L:9141182-9141302 1.0000 120 chr2L:2185480-2185600 1.0000 120 chr2L:2478472-2478592 1.0000 120 chrX:1979164-1979284 1.0000 120 chr2L:20716871-20716991 1.0000 120 chr3R:7992199-7992319 1.0000 120 chr3R:24777271-24777391 1.0000 120 chr3L:1688271-1688391 1.0000 120 chr3L:20562783-20562903 1.0000 120 chr2R:17243780-17243900 1.0000 120 chr2R:21801056-21801176 1.0000 120 chr3L:18146972-18147092 1.0000 120 chr3L:12060256-12060376 1.0000 120 chr3L:15708671-15708791 1.0000 120 chr2L:3731173-3731293 1.0000 120 chr2L:20943274-20943394 1.0000 120 chr3R:28842075-28842195 1.0000 120 chr2L:14318728-14318848 1.0000 120 chr3R:29982149-29982269 1.0000 120 chr3R:14720265-14720385 1.0000 120 chr3R:24204171-24204291 1.0000 120 chr3L:8384097-8384217 1.0000 120 chr3R:29755403-29755523 1.0000 120 chr3R:30828550-30828670 1.0000 120 chr3L:21224439-21224559 1.0000 120 chr2R:8152561-8152681 1.0000 120 chrX:4108163-4108283 1.0000 120 chr2L:3371544-3371664 1.0000 120 chrX:13911297-13911417 1.0000 120 chrX:724616-724736 1.0000 120 chr2L:5495057-5495177 1.0000 120 chr3L:22106823-22106943 1.0000 120 chr3L:20610573-20610693 1.0000 120 chr3R:31251488-31251608 1.0000 120 chrX:293419-293539 1.0000 120 chr3L:12025075-12025195 1.0000 120 chr2L:7938580-7938700 1.0000 120 chr3R:11595693-11595813 1.0000 120 chr2L:5090515-5090635 1.0000 120 chr3R:23324090-23324210 1.0000 120 chr3R:23737782-23737902 1.0000 120 chr2L:3881281-3881401 1.0000 120 chr3L:18096892-18097012 1.0000 120 chr2R:9024654-9024774 1.0000 120 chr3L:6263583-6263703 1.0000 120 chr3R:14280467-14280587 1.0000 120 chr2R:7112238-7112358 1.0000 120 chrX:18663516-18663636 1.0000 120 chr3L:20570268-20570388 1.0000 120 chr3R:6222255-6222375 1.0000 120 chrX:20489530-20489650 1.0000 120 chr3L:12109405-12109525 1.0000 120 chrX:16873167-16873287 1.0000 120 chr3L:6997076-6997196 1.0000 120 chr2R:15751753-15751873 1.0000 120 chr3L:17587984-17588104 1.0000 120 chr2R:8062107-8062227 1.0000 120 chr3R:17442320-17442440 1.0000 120 chr2L:664442-664562 1.0000 120 chr3R:5330472-5330592 1.0000 120 chr2L:14635159-14635279 1.0000 120 chr2L:7956374-7956494 1.0000 120 chr3L:10792029-10792149 1.0000 120 chr3R:6214359-6214479 1.0000 120 chr3R:21703499-21703619 1.0000 120 chr3R:28850797-28850917 1.0000 120 chr3R:19996556-19996676 1.0000 120 chr3R:23408039-23408159 1.0000 120 chr3L:8423272-8423392 1.0000 120 chr2R:7744737-7744857 1.0000 120 chr2R:10216584-10216704 1.0000 120 chr3L:10796060-10796180 1.0000 120 chr3L:21716073-21716193 1.0000 120 chrX:5002896-5003016 1.0000 120 chr3L:8319274-8319394 1.0000 120 chr3R:14486617-14486737 1.0000 120 chr3R:5324257-5324377 1.0000 120 chr3L:8782113-8782233 1.0000 120 chr2R:7173172-7173292 1.0000 120 chr3L:3283431-3283551 1.0000 120 chr2R:18901738-18901858 1.0000 120 chr2R:9032837-9032957 1.0000 120 chrX:2220011-2220131 1.0000 120 chr2R:23761512-23761632 1.0000 120 chr3L:3657022-3657142 1.0000 120 chr3L:741850-741970 1.0000 120 chr2L:15474498-15474618 1.0000 120 chr2R:15599991-15600111 1.0000 120 chr2R:23057010-23057130 1.0000 120 chr3R:14455570-14455690 1.0000 120 chrX:4170624-4170744 1.0000 120 chr3R:14761209-14761329 1.0000 120 chr3R:15541055-15541175 1.0000 120 chr3L:13180476-13180596 1.0000 120 chr2R:11763091-11763211 1.0000 120 chr3L:21046226-21046346 1.0000 120 chrX:10960016-10960136 1.0000 120 chr3L:9745509-9745629 1.0000 120 chr2L:4619338-4619458 1.0000 120 chr2L:9505858-9505978 1.0000 120 chr3R:31767653-31767773 1.0000 120 chr3R:23417807-23417927 1.0000 120 chrX:1988831-1988951 1.0000 120 chr3L:3419757-3419877 1.0000 120 chr3L:9765390-9765510 1.0000 120 chr3L:18628213-18628333 1.0000 120 chr2R:11315488-11315608 1.0000 120 chr3R:29847258-29847378 1.0000 120 chr2L:16803733-16803853 1.0000 120 chr2L:18752903-18753023 1.0000 120 chr2L:18493243-18493363 1.0000 120 chr3L:21229903-21230023 1.0000 120 chr3R:8107038-8107158 1.0000 120 chrX:11736583-11736703 1.0000 120 chr2L:1156782-1156902 1.0000 120 chr3R:11606826-11606946 1.0000 120 chr2R:22142212-22142332 1.0000 120 chr2L:18005639-18005759 1.0000 120 chrX:6357139-6357259 1.0000 120 chr2L:3635558-3635678 1.0000 120 chr3R:13857467-13857587 1.0000 120 chr3R:30567351-30567471 1.0000 120 chrX:22509182-22509302 1.0000 120 chr3R:22150076-22150196 1.0000 120 chrX:4965807-4965927 1.0000 120 chr3R:8470716-8470836 1.0000 120 chr3R:8234036-8234156 1.0000 120 chr3R:31319976-31320096 1.0000 120 chr3R:15806516-15806636 1.0000 120 chr2L:18331785-18331905 1.0000 120 chr3L:19196850-19196970 1.0000 120 chr2R:18353617-18353737 1.0000 120 chr2L:7598746-7598866 1.0000 120 chr3R:26019359-26019479 1.0000 120 chr3L:13215030-13215150 1.0000 120 chrX:15156433-15156553 1.0000 120 chr3L:6453606-6453726 1.0000 120 chr3R:20836469-20836589 1.0000 120 chr3L:11444313-11444433 1.0000 120 chr2L:21246817-21246937 1.0000 120 chr2L:604229-604349 1.0000 120 chr2L:18751494-18751614 1.0000 120 chr3R:28629253-28629373 1.0000 120 chr3R:23416691-23416811 1.0000 120 chr3L:3536681-3536801 1.0000 120 chr2R:17635146-17635266 1.0000 120 chr3R:6664929-6665049 1.0000 120 chr3R:12381474-12381594 1.0000 120 chr2R:23000793-23000913 1.0000 120 chr3L:7632964-7633084 1.0000 120 chrX:21073787-21073907 1.0000 120 chrX:3454842-3454962 1.0000 120 chr2R:7282229-7282349 1.0000 120 chr2L:16804533-16804653 1.0000 120 chr3L:564079-564199 1.0000 120 chr3R:6233201-6233321 1.0000 120 chr3L:756525-756645 1.0000 120 chr2R:22142414-22142534 1.0000 120 chr3R:30312664-30312784 1.0000 120 chr3L:19011283-19011403 1.0000 120 chrX:20130592-20130712 1.0000 120 chr3R:24886639-24886759 1.0000 120 chr2L:4065333-4065453 1.0000 120 chr2R:10847448-10847568 1.0000 120 chr3R:15113747-15113867 1.0000 120 chr3L:17981255-17981375 1.0000 120 chr2R:22119866-22119986 1.0000 120 chr3R:23391046-23391166 1.0000 120 chr3R:30344704-30344824 1.0000 120 chr2L:7949171-7949291 1.0000 120 chr2R:15483097-15483217 1.0000 120 chr3L:5626618-5626738 1.0000 120 chr2L:11014846-11014966 1.0000 120 chr2R:22148049-22148169 1.0000 120 chr2L:243954-244074 1.0000 120 chr3L:2145174-2145294 1.0000 120 chr2R:19904083-19904203 1.0000 120 chr2R:18243964-18244084 1.0000 120 chr3L:11536907-11537027 1.0000 120 chr2R:12984067-12984187 1.0000 120 chr3L:10376705-10376825 1.0000 120 chr2L:20340783-20340903 1.0000 120 chr3R:14279717-14279837 1.0000 120 chrX:15123537-15123657 1.0000 120 chr3L:10903557-10903677 1.0000 120 chr2R:23020473-23020593 1.0000 120 chrX:4959042-4959162 1.0000 120 chrX:15639170-15639290 1.0000 120 chrX:14211773-14211893 1.0000 120 chrX:17692960-17693080 1.0000 120 chr2L:11074097-11074217 1.0000 120 chr2L:1926064-1926184 1.0000 120 chr2L:20370313-20370433 1.0000 120 chr3R:27181239-27181359 1.0000 120 chr3R:15567116-15567236 1.0000 120 chr2L:17427268-17427388 1.0000 120 chrX:3739307-3739427 1.0000 120 chr2R:5496142-5496262 1.0000 120 chr3L:793878-793998 1.0000 120 chrX:17679775-17679895 1.0000 120 chr3L:10709270-10709390 1.0000 120 chr2R:23024307-23024427 1.0000 120 chr3L:16463961-16464081 1.0000 120 chr3L:1900832-1900952 1.0000 120 chr3L:10396676-10396796 1.0000 120 chr3R:21733082-21733202 1.0000 120 chr2R:14345503-14345623 1.0000 120 chr2L:20335067-20335187 1.0000 120 chr2R:8646556-8646676 1.0000 120 chr3L:16892829-16892949 1.0000 120 chr3R:13952437-13952557 1.0000 120 chrX:23071333-23071453 1.0000 120 chr3R:15927315-15927435 1.0000 120 chr2R:17077003-17077123 1.0000 120 chr2L:7513784-7513904 1.0000 120 chr3R:31314621-31314741 1.0000 120 chr3L:6308761-6308881 1.0000 120 chrX:4999162-4999282 1.0000 120 chrX:6662977-6663097 1.0000 120 chr3R:16336457-16336577 1.0000 120 chr2R:14326164-14326284 1.0000 120 chr3L:16748515-16748635 1.0000 120 chrX:3423509-3423629 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_CG32006/ -dna -nmotifs 5 -w 8 -maxsize 250000 -nostatus ../result/final_prediction/fly/fasta/RankLinear8.0_60/CG32006.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 0.351 C 0.148 G 0.146 T 0.355 Background letter frequencies (from file dataset with add-one prior applied): A 0.351 C 0.148 G 0.146 T 0.355 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF GGGGGSTG MEME-1 width = 8 sites = 2 llr = 28 E-value = 2.8e+003 ******************************************************************************** -------------------------------------------------------------------------------- Motif GGGGGSTG MEME-1 Description -------------------------------------------------------------------------------- Simplified A :::::::: pos.-specific C :::::5:: probability G aaaaa5:a matrix T ::::::a: bits 2.8 ***** * 2.5 ***** * 2.2 ***** * 1.9 ***** * Relative 1.7 ****** * Entropy 1.4 ******** (19.9 bits) 1.1 ******** 0.8 ******** 0.6 ******** 0.3 ******** 0.0 -------- Multilevel GGGGGCTG consensus G sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGGGGSTG MEME-1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr2R:11763091-11763211 99 1.01e-06 AGTATTTCTA GGGGGGTG AAGCGCTACT chr3R:29755403-29755523 9 1.01e-06 TGGCCAAA GGGGGCTG TTTGAGAATA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGGGGSTG MEME-1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr2R:11763091-11763211 1e-06 98_[+1]_14 chr3R:29755403-29755523 1e-06 8_[+1]_104 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGGGGSTG MEME-1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF GGGGGSTG width=8 seqs=2 chr2R:11763091-11763211 ( 99) GGGGGGTG 1 chr3R:29755403-29755523 ( 9) GGGGGCTG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGGGGSTG MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 28250 bayes= 13.7859 E= 2.8e+003 -765 -765 277 -765 -765 -765 277 -765 -765 -765 277 -765 -765 -765 277 -765 -765 -765 277 -765 -765 175 177 -765 -765 -765 -765 149 -765 -765 277 -765 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGGGGSTG MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 2 E= 2.8e+003 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 0.500000 0.500000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGGGGSTG MEME-1 regular expression -------------------------------------------------------------------------------- GGGGG[CG]TG -------------------------------------------------------------------------------- Time 9.90 secs. ******************************************************************************** ******************************************************************************** MOTIF GCACTGGG MEME-2 width = 8 sites = 2 llr = 27 E-value = 1.6e+004 ******************************************************************************** -------------------------------------------------------------------------------- Motif GCACTGGG MEME-2 Description -------------------------------------------------------------------------------- Simplified A ::a::::: pos.-specific C :a:a:::: probability G a::::aaa matrix T ::::a::: bits 2.8 ** * *** 2.5 ** * *** 2.2 ** * *** 1.9 ** * *** Relative 1.7 ** * *** Entropy 1.4 ******** (19.6 bits) 1.1 ******** 0.8 ******** 0.6 ******** 0.3 ******** 0.0 -------- Multilevel GCACTGGG consensus sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCACTGGG MEME-2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr3L:10792029-10792149 32 1.24e-06 GGGAGGAAGT GCACTGGG AGAAATCTCA chr3R:24204171-24204291 99 1.24e-06 TTTCCCCAGT GCACTGGG TGGCAGTGGC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCACTGGG MEME-2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr3L:10792029-10792149 1.2e-06 31_[+2]_81 chr3R:24204171-24204291 1.2e-06 98_[+2]_14 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCACTGGG MEME-2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF GCACTGGG width=8 seqs=2 chr3L:10792029-10792149 ( 32) GCACTGGG 1 chr3R:24204171-24204291 ( 99) GCACTGGG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCACTGGG MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 28250 bayes= 13.7859 E= 1.6e+004 -765 -765 277 -765 -765 275 -765 -765 150 -765 -765 -765 -765 275 -765 -765 -765 -765 -765 149 -765 -765 277 -765 -765 -765 277 -765 -765 -765 277 -765 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCACTGGG MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 2 E= 1.6e+004 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 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 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCACTGGG MEME-2 regular expression -------------------------------------------------------------------------------- GCACTGGG -------------------------------------------------------------------------------- Time 16.15 secs. ******************************************************************************** ******************************************************************************** MOTIF GAGCGCTG MEME-3 width = 8 sites = 2 llr = 27 E-value = 1.6e+004 ******************************************************************************** -------------------------------------------------------------------------------- Motif GAGCGCTG MEME-3 Description -------------------------------------------------------------------------------- Simplified A :a:::::: pos.-specific C :::a:a:: probability G a:a:a::a matrix T ::::::a: bits 2.8 * **** * 2.5 * **** * 2.2 * **** * 1.9 * **** * Relative 1.7 * **** * Entropy 1.4 ******** (19.6 bits) 1.1 ******** 0.8 ******** 0.6 ******** 0.3 ******** 0.0 -------- Multilevel GAGCGCTG consensus sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GAGCGCTG MEME-3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chrX:22509182-22509302 94 1.24e-06 GATCGTATTT GAGCGCTG TTTAAAGGAA chr2R:16742121-16742241 96 1.24e-06 ACCAATTATT GAGCGCTG AAAAATCTTG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GAGCGCTG MEME-3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrX:22509182-22509302 1.2e-06 93_[+3]_19 chr2R:16742121-16742241 1.2e-06 95_[+3]_17 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GAGCGCTG MEME-3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF GAGCGCTG width=8 seqs=2 chrX:22509182-22509302 ( 94) GAGCGCTG 1 chr2R:16742121-16742241 ( 96) GAGCGCTG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GAGCGCTG MEME-3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 28250 bayes= 13.7859 E= 1.6e+004 -765 -765 277 -765 150 -765 -765 -765 -765 -765 277 -765 -765 275 -765 -765 -765 -765 277 -765 -765 275 -765 -765 -765 -765 -765 149 -765 -765 277 -765 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GAGCGCTG MEME-3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 2 E= 1.6e+004 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GAGCGCTG MEME-3 regular expression -------------------------------------------------------------------------------- GAGCGCTG -------------------------------------------------------------------------------- Time 22.39 secs. ******************************************************************************** ******************************************************************************** MOTIF GGGMGTGS MEME-4 width = 8 sites = 2 llr = 25 E-value = 3.6e+004 ******************************************************************************** -------------------------------------------------------------------------------- Motif GGGMGTGS MEME-4 Description -------------------------------------------------------------------------------- Simplified A :::5:::: pos.-specific C :::5:::5 probability G aaa:a:a5 matrix T :::::a:: bits 2.8 *** * * 2.5 *** * * 2.2 *** * * 1.9 *** * * Relative 1.7 *** * ** Entropy 1.4 *** **** (18.3 bits) 1.1 ******** 0.8 ******** 0.6 ******** 0.3 ******** 0.0 -------- Multilevel GGGAGTGC consensus C G sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGGMGTGS MEME-4 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr2R:9024654-9024774 46 1.02e-06 AGATGGGTTC GGGCGTGG TTTGTTGTAT chr3R:11595693-11595813 14 3.45e-06 ATGAAAAACT GGGAGTGC GTTCATCGGA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGGMGTGS MEME-4 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr2R:9024654-9024774 1e-06 45_[+4]_67 chr3R:11595693-11595813 3.5e-06 13_[+4]_99 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGGMGTGS MEME-4 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF GGGMGTGS width=8 seqs=2 chr2R:9024654-9024774 ( 46) GGGCGTGG 1 chr3R:11595693-11595813 ( 14) GGGAGTGC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGGMGTGS MEME-4 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 28250 bayes= 13.7859 E= 3.6e+004 -765 -765 277 -765 -765 -765 277 -765 -765 -765 277 -765 51 175 -765 -765 -765 -765 277 -765 -765 -765 -765 149 -765 -765 277 -765 -765 175 177 -765 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGGMGTGS MEME-4 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 2 E= 3.6e+004 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.500000 0.500000 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 0.500000 0.500000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGGMGTGS MEME-4 regular expression -------------------------------------------------------------------------------- GGG[AC]GTG[CG] -------------------------------------------------------------------------------- Time 28.66 secs. ******************************************************************************** ******************************************************************************** MOTIF NGCATTGC MEME-5 width = 8 sites = 15 llr = 147 E-value = 4.3e+004 ******************************************************************************** -------------------------------------------------------------------------------- Motif NGCATTGC MEME-5 Description -------------------------------------------------------------------------------- Simplified A 2::8:::: pos.-specific C 3:a2:::8 probability G 3a::3:a2 matrix T 2:::7a:: bits 2.8 ** * 2.5 ** * 2.2 ** * 1.9 ** ** Relative 1.7 ** ** Entropy 1.4 ** *** (14.2 bits) 1.1 ******* 0.8 ******* 0.6 ******* 0.3 ******** 0.0 -------- Multilevel CGCATTGC consensus G CG G sequence A T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif NGCATTGC MEME-5 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr2L:604229-604349 11 3.06e-06 TGTAAGAAAT CGCATTGC TCGATAGTCC chr2L:20370313-20370433 113 4.31e-06 CTGAATTTCT CGCAGTGC chr3R:30567351-30567471 49 7.33e-06 TCAACATAAA GGCATTGC GTGTGAATGG chr3R:17442320-17442440 47 8.57e-06 CCAAAAGTTC GGCAGTGC ATTGAAATAA chr2L:14370864-14370984 83 9.86e-06 GCCACTAGTC CGCCTTGC TGATGGCTTT chr2R:11315488-11315608 50 1.17e-05 AAGACTGTAA GGCCTTGC GTCGAAGATG chrX:6357139-6357259 80 1.52e-05 TGCGGTTTGC CGCATTGG CTACAAAACG chr3R:23408039-23408159 102 1.52e-05 GATCTGCTAC CGCATTGG TTTAGAGAAT chr2R:14326164-14326284 112 3.10e-05 TCCGTGTGGC TGCATTGC A chr3L:8319274-8319394 49 3.10e-05 TTAGGAAGTC AGCATTGC AAATATTTAA chr3L:8384097-8384217 62 3.10e-05 TCTGCACAGC TGCATTGC TCCACTTTGA chr3L:19329630-19329750 80 3.10e-05 GAGGAACAAC AGCATTGC AGAAAGACAA chr3R:5324257-5324377 102 4.00e-05 TAGTATTTGT AGCAGTGC TAGATACCAT chr3R:24204171-24204291 108 4.12e-05 TGCACTGGGT GGCAGTGG CAGCA chr2L:16804533-16804653 67 4.92e-05 AACATATATT TGCCTTGC ATATTTCTTC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif NGCATTGC MEME-5 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr2L:604229-604349 3.1e-06 10_[+5]_102 chr2L:20370313-20370433 4.3e-06 112_[+5] chr3R:30567351-30567471 7.3e-06 48_[+5]_64 chr3R:17442320-17442440 8.6e-06 46_[+5]_66 chr2L:14370864-14370984 9.9e-06 82_[+5]_30 chr2R:11315488-11315608 1.2e-05 49_[+5]_63 chrX:6357139-6357259 1.5e-05 79_[+5]_33 chr3R:23408039-23408159 1.5e-05 101_[+5]_11 chr2R:14326164-14326284 3.1e-05 111_[+5]_1 chr3L:8319274-8319394 3.1e-05 48_[+5]_64 chr3L:8384097-8384217 3.1e-05 61_[+5]_51 chr3L:19329630-19329750 3.1e-05 79_[+5]_33 chr3R:5324257-5324377 4e-05 101_[+5]_11 chr3R:24204171-24204291 4.1e-05 107_[+5]_5 chr2L:16804533-16804653 4.9e-05 66_[+5]_46 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif NGCATTGC MEME-5 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF NGCATTGC width=8 seqs=15 chr2L:604229-604349 ( 11) CGCATTGC 1 chr2L:20370313-20370433 ( 113) CGCAGTGC 1 chr3R:30567351-30567471 ( 49) GGCATTGC 1 chr3R:17442320-17442440 ( 47) GGCAGTGC 1 chr2L:14370864-14370984 ( 83) CGCCTTGC 1 chr2R:11315488-11315608 ( 50) GGCCTTGC 1 chrX:6357139-6357259 ( 80) CGCATTGG 1 chr3R:23408039-23408159 ( 102) CGCATTGG 1 chr2R:14326164-14326284 ( 112) TGCATTGC 1 chr3L:8319274-8319394 ( 49) AGCATTGC 1 chr3L:8384097-8384217 ( 62) TGCATTGC 1 chr3L:19329630-19329750 ( 80) AGCATTGC 1 chr3R:5324257-5324377 ( 102) AGCAGTGC 1 chr3R:24204171-24204291 ( 108) GGCAGTGG 1 chr2L:16804533-16804653 ( 67) TGCCTTGC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif NGCATTGC MEME-5 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 28250 bayes= 12.5841 E= 4.3e+004 -81 117 87 -83 -1055 -1055 277 -1055 -1055 276 -1055 -1055 119 43 -1055 -1055 -1055 -1055 87 105 -1055 -1055 -1055 150 -1055 -1055 277 -1055 -1055 243 45 -1055 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif NGCATTGC MEME-5 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 15 E= 4.3e+004 0.200000 0.333333 0.266667 0.200000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.800000 0.200000 0.000000 0.000000 0.000000 0.000000 0.266667 0.733333 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.800000 0.200000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif NGCATTGC MEME-5 regular expression -------------------------------------------------------------------------------- [CGAT]GC[AC][TG]TG[CG] -------------------------------------------------------------------------------- Time 34.90 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr2R:12603475-12603595 9.85e-01 120 chr2L:17492793-17492913 9.95e-01 120 chr3L:5609608-5609728 1.00e-01 [+2(4.91e-05)]_112 chr3R:19808171-19808291 1.00e+00 120 chr3L:1200474-1200594 8.15e-01 120 chr2R:16742121-16742241 8.51e-04 95_[+3(1.24e-06)]_17 chr3L:8422407-8422527 1.72e-01 120 chr2R:7734085-7734205 1.68e-01 120 chrX:10953377-10953497 1.00e+00 120 chr2L:13925806-13925926 4.99e-02 120 chr3R:8948193-8948313 9.81e-01 120 chr2R:7905093-7905213 7.83e-01 120 chr2L:20295995-20296115 9.49e-01 120 chr3L:19329630-19329750 7.00e-02 79_[+5(3.10e-05)]_33 chr2R:20024376-20024496 9.95e-01 120 chr3L:10398821-10398941 9.92e-01 120 chr2L:19307778-19307898 9.11e-01 120 chr3R:6215140-6215260 4.00e-01 120 chr3R:24219238-24219358 9.29e-01 120 chr2L:15321596-15321716 5.46e-01 120 chr3R:15922724-15922844 4.47e-01 120 chr2R:13769489-13769609 5.09e-01 120 chr2L:14370864-14370984 4.92e-02 82_[+5(9.86e-06)]_30 chr3L:1905392-1905512 7.14e-01 120 chr2R:8353392-8353512 1.00e+00 120 chr2L:11505390-11505510 1.00e+00 120 chr2R:12413254-12413374 1.10e-01 120 chr2L:9141182-9141302 6.49e-01 120 chr2L:2185480-2185600 6.02e-01 120 chr2L:2478472-2478592 1.77e-01 120 chrX:1979164-1979284 4.97e-01 120 chr2L:20716871-20716991 3.22e-01 120 chr3R:7992199-7992319 2.70e-02 4_[+4(1.12e-05)]_108 chr3R:24777271-24777391 9.79e-01 120 chr3L:1688271-1688391 6.97e-01 120 chr3L:20562783-20562903 6.37e-01 120 chr2R:17243780-17243900 9.49e-01 120 chr2R:21801056-21801176 1.51e-01 120 chr3L:18146972-18147092 7.01e-01 120 chr3L:12060256-12060376 9.91e-01 120 chr3L:15708671-15708791 9.72e-01 120 chr2L:3731173-3731293 9.30e-01 120 chr2L:20943274-20943394 2.63e-02 120 chr3R:28842075-28842195 4.73e-01 120 chr2L:14318728-14318848 9.20e-01 120 chr3R:29982149-29982269 1.92e-01 120 chr3R:14720265-14720385 1.90e-01 120 chr3R:24204171-24204291 6.43e-08 98_[+2(1.24e-06)]_1_[+5(4.12e-05)]_\ 5 chr3L:8384097-8384217 2.69e-02 61_[+5(3.10e-05)]_51 chr3R:29755403-29755523 3.29e-04 8_[+1(1.01e-06)]_104 chr3R:30828550-30828670 5.13e-01 120 chr3L:21224439-21224559 9.79e-01 120 chr2R:8152561-8152681 9.62e-01 120 chrX:4108163-4108283 2.56e-02 120 chr2L:3371544-3371664 3.40e-01 120 chrX:13911297-13911417 1.84e-02 120 chrX:724616-724736 4.09e-01 120 chr2L:5495057-5495177 3.08e-01 120 chr3L:22106823-22106943 9.80e-01 120 chr3L:20610573-20610693 9.98e-01 120 chr3R:31251488-31251608 9.82e-01 120 chrX:293419-293539 6.52e-01 120 chr3L:12025075-12025195 9.84e-01 120 chr2L:7938580-7938700 8.48e-01 120 chr3R:11595693-11595813 1.66e-04 13_[+4(3.45e-06)]_99 chr2L:5090515-5090635 9.40e-01 120 chr3R:23324090-23324210 8.19e-01 120 chr3R:23737782-23737902 4.30e-01 120 chr2L:3881281-3881401 1.78e-01 120 chr3L:18096892-18097012 6.62e-01 120 chr2R:9024654-9024774 2.02e-04 45_[+4(1.02e-06)]_67 chr3L:6263583-6263703 1.87e-01 120 chr3R:14280467-14280587 7.78e-01 120 chr2R:7112238-7112358 2.86e-01 120 chrX:18663516-18663636 9.90e-01 120 chr3L:20570268-20570388 6.08e-01 120 chr3R:6222255-6222375 6.48e-01 120 chrX:20489530-20489650 5.83e-02 59_[+1(4.08e-05)]_53 chr3L:12109405-12109525 6.57e-01 120 chrX:16873167-16873287 9.27e-01 120 chr3L:6997076-6997196 5.99e-01 120 chr2R:15751753-15751873 3.46e-01 120 chr3L:17587984-17588104 3.57e-01 120 chr2R:8062107-8062227 8.09e-01 120 chr3R:17442320-17442440 2.63e-03 46_[+5(8.57e-06)]_66 chr2L:664442-664562 7.59e-01 120 chr3R:5330472-5330592 9.42e-01 120 chr2L:14635159-14635279 1.00e+00 120 chr2L:7956374-7956494 7.50e-01 120 chr3L:10792029-10792149 2.29e-06 31_[+2(1.24e-06)]_81 chr3R:6214359-6214479 5.81e-02 120 chr3R:21703499-21703619 9.00e-01 120 chr3R:28850797-28850917 5.17e-01 120 chr3R:19996556-19996676 5.64e-01 120 chr3R:23408039-23408159 5.37e-02 101_[+5(1.52e-05)]_11 chr3L:8423272-8423392 9.97e-01 120 chr2R:7744737-7744857 4.45e-01 120 chr2R:10216584-10216704 1.00e+00 120 chr3L:10796060-10796180 7.73e-01 120 chr3L:21716073-21716193 2.86e-01 120 chrX:5002896-5003016 4.95e-01 120 chr3L:8319274-8319394 5.02e-02 48_[+5(3.10e-05)]_64 chr3R:14486617-14486737 9.59e-01 120 chr3R:5324257-5324377 3.42e-02 101_[+5(4.00e-05)]_11 chr3L:8782113-8782233 5.00e-01 120 chr2R:7173172-7173292 9.13e-01 120 chr3L:3283431-3283551 7.02e-01 120 chr2R:18901738-18901858 5.48e-01 120 chr2R:9032837-9032957 8.34e-01 120 chrX:2220011-2220131 1.16e-01 120 chr2R:23761512-23761632 6.25e-01 120 chr3L:3657022-3657142 2.05e-01 120 chr3L:741850-741970 9.39e-01 120 chr2L:15474498-15474618 9.95e-01 120 chr2R:15599991-15600111 9.65e-01 120 chr2R:23057010-23057130 2.33e-03 13_[+2(4.91e-05)]_8_[+3(4.91e-05)]_\ 83 chr3R:14455570-14455690 5.46e-01 120 chrX:4170624-4170744 7.36e-01 120 chr3R:14761209-14761329 3.40e-01 120 chr3R:15541055-15541175 1.24e-01 32_[+5(9.70e-05)]_80 chr3L:13180476-13180596 9.63e-01 120 chr2R:11763091-11763211 6.44e-06 98_[+1(1.01e-06)]_14 chr3L:21046226-21046346 3.61e-01 120 chrX:10960016-10960136 9.88e-01 120 chr3L:9745509-9745629 9.64e-01 120 chr2L:4619338-4619458 9.56e-01 120 chr2L:9505858-9505978 8.97e-02 120 chr3R:31767653-31767773 1.32e-02 120 chr3R:23417807-23417927 4.48e-01 120 chrX:1988831-1988951 4.44e-02 120 chr3L:3419757-3419877 9.93e-01 120 chr3L:9765390-9765510 9.99e-01 120 chr3L:18628213-18628333 2.53e-01 120 chr2R:11315488-11315608 2.42e-03 49_[+5(1.17e-05)]_63 chr3R:29847258-29847378 2.74e-01 120 chr2L:16803733-16803853 9.73e-01 120 chr2L:18752903-18753023 8.89e-01 120 chr2L:18493243-18493363 1.00e+00 120 chr3L:21229903-21230023 1.02e-01 120 chr3R:8107038-8107158 6.03e-01 120 chrX:11736583-11736703 6.03e-02 120 chr2L:1156782-1156902 6.57e-02 120 chr3R:11606826-11606946 9.49e-01 120 chr2R:22142212-22142332 9.57e-02 120 chr2L:18005639-18005759 7.57e-01 120 chrX:6357139-6357259 9.13e-03 79_[+5(1.52e-05)]_33 chr2L:3635558-3635678 9.99e-01 120 chr3R:13857467-13857587 1.31e-01 120 chr3R:30567351-30567471 2.51e-03 48_[+5(7.33e-06)]_64 chrX:22509182-22509302 4.27e-04 93_[+3(1.24e-06)]_19 chr3R:22150076-22150196 1.00e+00 120 chrX:4965807-4965927 6.75e-01 120 chr3R:8470716-8470836 8.68e-01 120 chr3R:8234036-8234156 8.94e-01 120 chr3R:31319976-31320096 9.15e-01 120 chr3R:15806516-15806636 9.88e-01 120 chr2L:18331785-18331905 9.31e-01 120 chr3L:19196850-19196970 4.93e-01 120 chr2R:18353617-18353737 6.49e-01 120 chr2L:7598746-7598866 6.42e-01 120 chr3R:26019359-26019479 6.38e-01 120 chr3L:13215030-13215150 9.53e-01 120 chrX:15156433-15156553 6.89e-01 120 chr3L:6453606-6453726 9.26e-01 120 chr3R:20836469-20836589 5.48e-01 120 chr3L:11444313-11444433 8.49e-01 120 chr2L:21246817-21246937 9.99e-01 120 chr2L:604229-604349 3.36e-02 10_[+5(3.06e-06)]_102 chr2L:18751494-18751614 1.00e+00 120 chr3R:28629253-28629373 5.70e-01 120 chr3R:23416691-23416811 9.56e-01 120 chr3L:3536681-3536801 7.75e-01 120 chr2R:17635146-17635266 9.99e-01 120 chr3R:6664929-6665049 2.09e-01 120 chr3R:12381474-12381594 9.95e-01 120 chr2R:23000793-23000913 1.40e-02 11_[+2(4.91e-05)]_101 chr3L:7632964-7633084 9.98e-01 120 chrX:21073787-21073907 8.61e-01 120 chrX:3454842-3454962 9.50e-01 120 chr2R:7282229-7282349 9.67e-01 120 chr2L:16804533-16804653 3.16e-01 66_[+5(4.92e-05)]_46 chr3L:564079-564199 1.88e-01 120 chr3R:6233201-6233321 1.42e-01 120 chr3L:756525-756645 3.96e-01 120 chr2R:22142414-22142534 7.73e-02 120 chr3R:30312664-30312784 2.01e-02 89_[+5(6.78e-05)]_23 chr3L:19011283-19011403 9.91e-01 120 chrX:20130592-20130712 3.53e-01 120 chr3R:24886639-24886759 9.96e-01 120 chr2L:4065333-4065453 9.22e-01 120 chr2R:10847448-10847568 1.00e+00 120 chr3R:15113747-15113867 7.34e-01 120 chr3L:17981255-17981375 7.87e-01 120 chr2R:22119866-22119986 2.06e-01 120 chr3R:23391046-23391166 9.11e-01 120 chr3R:30344704-30344824 5.71e-01 120 chr2L:7949171-7949291 9.72e-01 120 chr2R:15483097-15483217 4.97e-01 120 chr3L:5626618-5626738 6.01e-01 120 chr2L:11014846-11014966 6.24e-01 120 chr2R:22148049-22148169 5.45e-03 120 chr2L:243954-244074 6.10e-01 120 chr3L:2145174-2145294 1.06e-01 120 chr2R:19904083-19904203 9.99e-01 120 chr2R:18243964-18244084 9.99e-01 120 chr3L:11536907-11537027 6.53e-01 120 chr2R:12984067-12984187 9.20e-01 120 chr3L:10376705-10376825 4.35e-01 120 chr2L:20340783-20340903 7.49e-02 120 chr3R:14279717-14279837 1.26e-02 120 chrX:15123537-15123657 8.95e-01 120 chr3L:10903557-10903677 9.76e-01 120 chr2R:23020473-23020593 9.43e-01 120 chrX:4959042-4959162 9.98e-01 120 chrX:15639170-15639290 5.16e-01 120 chrX:14211773-14211893 4.89e-01 120 chrX:17692960-17693080 4.97e-02 120 chr2L:11074097-11074217 9.54e-01 120 chr2L:1926064-1926184 7.95e-01 120 chr2L:20370313-20370433 2.86e-02 112_[+5(4.31e-06)] chr3R:27181239-27181359 9.97e-01 120 chr3R:15567116-15567236 3.06e-01 120 chr2L:17427268-17427388 5.59e-01 120 chrX:3739307-3739427 9.80e-01 120 chr2R:5496142-5496262 9.98e-01 120 chr3L:793878-793998 2.55e-01 120 chrX:17679775-17679895 2.81e-01 120 chr3L:10709270-10709390 1.42e-01 120 chr2R:23024307-23024427 9.90e-01 120 chr3L:16463961-16464081 1.36e-01 120 chr3L:1900832-1900952 9.67e-01 120 chr3L:10396676-10396796 9.53e-01 120 chr3R:21733082-21733202 5.57e-01 120 chr2R:14345503-14345623 9.50e-01 120 chr2L:20335067-20335187 9.69e-01 120 chr2R:8646556-8646676 6.21e-01 120 chr3L:16892829-16892949 3.38e-01 120 chr3R:13952437-13952557 9.86e-01 120 chrX:23071333-23071453 1.44e-01 120 chr3R:15927315-15927435 1.89e-01 120 chr2R:17077003-17077123 9.98e-01 120 chr2L:7513784-7513904 7.06e-01 120 chr3R:31314621-31314741 1.28e-01 120 chr3L:6308761-6308881 9.67e-01 120 chrX:4999162-4999282 6.90e-01 120 chrX:6662977-6663097 8.60e-01 120 chr3R:16336457-16336577 4.07e-01 120 chr2R:14326164-14326284 3.94e-02 111_[+5(3.10e-05)]_1 chr3L:16748515-16748635 9.56e-01 120 chrX:3423509-3423629 1.47e-01 120 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (5) found. ******************************************************************************** CPU: c28n06.farnam.hpc.yale.internal ********************************************************************************