******************************************************************************** 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/eve.fasta CONTROL SEQUENCES= --none-- ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ chrX:3688731-3688851 1.0000 120 chr3L:9114894-9115014 1.0000 120 chr2L:11970496-11970616 1.0000 120 chr2R:22401171-22401291 1.0000 120 chr3R:9337246-9337366 1.0000 120 chr2R:9556986-9557106 1.0000 120 chr2L:14536480-14536600 1.0000 120 chr2R:5662409-5662529 1.0000 120 chr3R:29254921-29255041 1.0000 120 chr2R:15909120-15909240 1.0000 120 chr3R:26954878-26954998 1.0000 120 chr2L:14409084-14409204 1.0000 120 chr3R:21061178-21061298 1.0000 120 chr3R:6425072-6425192 1.0000 120 chr2R:11666059-11666179 1.0000 120 chr3R:9442123-9442243 1.0000 120 chr4:559596-559716 1.0000 120 chrX:6864713-6864833 1.0000 120 chr2R:23581536-23581656 1.0000 120 chr2L:20803197-20803317 1.0000 120 chr2R:9550649-9550769 1.0000 120 chr3L:12487745-12487865 1.0000 120 chrX:13375145-13375265 1.0000 120 chr3L:17486534-17486654 1.0000 120 chr2L:8091603-8091723 1.0000 120 chr3R:19001425-19001545 1.0000 120 chr3R:21058882-21059002 1.0000 120 chr3L:21014076-21014196 1.0000 120 chr2L:1446194-1446314 1.0000 120 chr3L:614365-614485 1.0000 120 chr2L:1461355-1461475 1.0000 120 chr3L:346121-346241 1.0000 120 chr3L:6695476-6695596 1.0000 120 chr3L:22362752-22362872 1.0000 120 chr2R:10517489-10517609 1.0000 120 chr3L:21045516-21045636 1.0000 120 chr2L:14477331-14477451 1.0000 120 chr3L:551986-552106 1.0000 120 chr2L:2732197-2732317 1.0000 120 chr3L:9124620-9124740 1.0000 120 chr2L:1737820-1737940 1.0000 120 chr3L:10844203-10844323 1.0000 120 chr2L:10590363-10590483 1.0000 120 chr2R:16617206-16617326 1.0000 120 chr3R:14034776-14034896 1.0000 120 chrX:15893602-15893722 1.0000 120 chrX:2362852-2362972 1.0000 120 chr3R:10601630-10601750 1.0000 120 chrX:15631130-15631250 1.0000 120 chr2R:12258833-12258953 1.0000 120 chr2R:13925093-13925213 1.0000 120 chr2R:19270588-19270708 1.0000 120 chrX:5417555-5417675 1.0000 120 chr3R:14740262-14740382 1.0000 120 chr2R:7746098-7746218 1.0000 120 chr2L:312110-312230 1.0000 120 chr2R:16716341-16716461 1.0000 120 chrX:19165807-19165927 1.0000 120 chr2R:15898667-15898787 1.0000 120 chr3L:469022-469142 1.0000 120 chr3R:19322536-19322656 1.0000 120 chr2L:3713650-3713770 1.0000 120 chr2L:225739-225859 1.0000 120 chr2R:11603998-11604118 1.0000 120 chr3R:9885352-9885472 1.0000 120 chr3L:7787517-7787637 1.0000 120 chr2L:3144385-3144505 1.0000 120 chr2L:482956-483076 1.0000 120 chr3L:8553794-8553914 1.0000 120 chr2L:2854901-2855021 1.0000 120 chr2R:19803893-19804013 1.0000 120 chr3R:13997465-13997585 1.0000 120 chr2R:5987973-5988093 1.0000 120 chr2R:12736968-12737088 1.0000 120 chr4:66810-66930 1.0000 120 chr3R:6474954-6475074 1.0000 120 chr2L:18319380-18319500 1.0000 120 chr2R:11658719-11658839 1.0000 120 chr3R:17055874-17055994 1.0000 120 chr3L:3383579-3383699 1.0000 120 chr2R:5992442-5992562 1.0000 120 chr2L:1657780-1657900 1.0000 120 chr2L:3146030-3146150 1.0000 120 chr3L:632748-632868 1.0000 120 chr2R:6117179-6117299 1.0000 120 chr3R:25515165-25515285 1.0000 120 chr3L:18030546-18030666 1.0000 120 chr3L:15698821-15698941 1.0000 120 chr2R:11650423-11650543 1.0000 120 chr3R:27149581-27149701 1.0000 120 chr3R:9502910-9503030 1.0000 120 chr3L:19019900-19020020 1.0000 120 chr3L:4121719-4121839 1.0000 120 chr3L:491294-491414 1.0000 120 chr3R:30815589-30815709 1.0000 120 chr2R:19167872-19167992 1.0000 120 chrX:18358481-18358601 1.0000 120 chr2L:16633644-16633764 1.0000 120 chr3L:3072856-3072976 1.0000 120 chr2R:25226927-25227047 1.0000 120 chr2R:11712524-11712644 1.0000 120 chr2L:18320635-18320755 1.0000 120 chr3L:18757694-18757814 1.0000 120 chr3R:13998308-13998428 1.0000 120 chr2R:8052322-8052442 1.0000 120 chr2R:18355167-18355287 1.0000 120 chr3L:473551-473671 1.0000 120 chr3R:21657857-21657977 1.0000 120 chr2L:1213744-1213864 1.0000 120 chr3L:1580857-1580977 1.0000 120 chr3L:10681378-10681498 1.0000 120 chr3R:10267733-10267853 1.0000 120 chr2R:16717501-16717621 1.0000 120 chr2R:6964282-6964402 1.0000 120 chr2R:13540453-13540573 1.0000 120 chrX:9551346-9551466 1.0000 120 chr2R:12539186-12539306 1.0000 120 chr2L:16545307-16545427 1.0000 120 chr3R:21659226-21659346 1.0000 120 chr2R:9309135-9309255 1.0000 120 chr2L:3100093-3100213 1.0000 120 chr2R:9549186-9549306 1.0000 120 chr3R:30782393-30782513 1.0000 120 chrX:1964577-1964697 1.0000 120 chr3R:9877297-9877417 1.0000 120 chr3L:19565197-19565317 1.0000 120 chr3L:4347583-4347703 1.0000 120 chr3R:5075221-5075341 1.0000 120 chr2L:1642609-1642729 1.0000 120 chr3R:14019100-14019220 1.0000 120 chr2L:511297-511417 1.0000 120 chr3R:23220969-23221089 1.0000 120 chr2L:55569-55689 1.0000 120 chrX:12574249-12574369 1.0000 120 chr2R:5495614-5495734 1.0000 120 chr3L:11488150-11488270 1.0000 120 chr2L:8735332-8735452 1.0000 120 chr2R:6159576-6159696 1.0000 120 chr3L:17488034-17488154 1.0000 120 chr2R:19415975-19416095 1.0000 120 chrX:3749262-3749382 1.0000 120 chr3L:8952109-8952229 1.0000 120 chr2L:13059662-13059782 1.0000 120 chr4:1038824-1038944 1.0000 120 chr2R:16833365-16833485 1.0000 120 chr3L:1570737-1570857 1.0000 120 chr4:957759-957879 1.0000 120 chr3R:9535344-9535464 1.0000 120 chr2L:491702-491822 1.0000 120 chr3R:10392529-10392649 1.0000 120 chr2L:14198514-14198634 1.0000 120 chr3R:24602355-24602475 1.0000 120 chr4:1009436-1009556 1.0000 120 chrX:688338-688458 1.0000 120 chr3R:17402103-17402223 1.0000 120 chr3R:11605176-11605296 1.0000 120 chr3L:13113658-13113778 1.0000 120 chr2L:1653907-1654027 1.0000 120 chr3R:32032962-32033082 1.0000 120 chrX:18919564-18919684 1.0000 120 chrX:17477136-17477256 1.0000 120 chr2L:159533-159653 1.0000 120 chr3R:21298367-21298487 1.0000 120 chr4:553280-553400 1.0000 120 chr2L:4996653-4996773 1.0000 120 chr2L:11060053-11060173 1.0000 120 chr2L:162440-162560 1.0000 120 chr4:155799-155919 1.0000 120 chr3R:16279637-16279757 1.0000 120 chr2L:21316881-21317001 1.0000 120 chr2L:2897873-2897993 1.0000 120 chr2L:9704882-9705002 1.0000 120 chr3R:10033095-10033215 1.0000 120 chr2R:12955524-12955644 1.0000 120 chr3R:17944423-17944543 1.0000 120 chr2R:15891611-15891731 1.0000 120 chr3L:2546472-2546592 1.0000 120 chr2R:13582390-13582510 1.0000 120 chr3L:12565555-12565675 1.0000 120 chr2L:20860223-20860343 1.0000 120 chr2L:16619044-16619164 1.0000 120 chr3R:9548515-9548635 1.0000 120 chr3R:20956359-20956479 1.0000 120 chr2R:7785350-7785470 1.0000 120 chr3L:8006387-8006507 1.0000 120 chr3R:5122287-5122407 1.0000 120 chrX:10513809-10513929 1.0000 120 chr3R:9446949-9447069 1.0000 120 chr3L:131004-131124 1.0000 120 chr3R:14059192-14059312 1.0000 120 chr3R:10276287-10276407 1.0000 120 chr4:833580-833700 1.0000 120 chr2R:25030563-25030683 1.0000 120 chr3R:5020820-5020940 1.0000 120 chr3R:5037808-5037928 1.0000 120 chr3R:15122659-15122779 1.0000 120 chrX:14211889-14212009 1.0000 120 chr3L:3786532-3786652 1.0000 120 chr3L:21048730-21048850 1.0000 120 chr3R:11762217-11762337 1.0000 120 chr2R:9668388-9668508 1.0000 120 chr3L:8832228-8832348 1.0000 120 chr3L:13114619-13114739 1.0000 120 chrX:19602148-19602268 1.0000 120 chr3R:10590527-10590647 1.0000 120 chr3R:29457898-29458018 1.0000 120 chr3R:30565979-30566099 1.0000 120 chr3L:2585142-2585262 1.0000 120 chr2R:6142019-6142139 1.0000 120 chr3R:15666487-15666607 1.0000 120 chr2R:5362447-5362567 1.0000 120 chr2L:8559067-8559187 1.0000 120 chr2R:10480931-10481051 1.0000 120 chr3R:23174208-23174328 1.0000 120 chr3L:4310711-4310831 1.0000 120 chr3L:5975612-5975732 1.0000 120 chr2L:18643649-18643769 1.0000 120 chr3R:9419817-9419937 1.0000 120 chr3L:2457203-2457323 1.0000 120 chr2R:17116656-17116776 1.0000 120 chr2R:7759490-7759610 1.0000 120 chr2L:5869276-5869396 1.0000 120 chr2R:5704319-5704439 1.0000 120 chr3R:13363870-13363990 1.0000 120 chr2R:25008390-25008510 1.0000 120 chr3L:22199509-22199629 1.0000 120 chr3L:4607186-4607306 1.0000 120 chr2L:10241116-10241236 1.0000 120 chrX:6872420-6872540 1.0000 120 chr2R:10526262-10526382 1.0000 120 chr3L:16689669-16689789 1.0000 120 chr3R:14289703-14289823 1.0000 120 chr3L:16985250-16985370 1.0000 120 chr3R:5279326-5279446 1.0000 120 chr2L:16353886-16354006 1.0000 120 chr2R:7757642-7757762 1.0000 120 chr3L:11254951-11255071 1.0000 120 chrX:3751507-3751627 1.0000 120 chr4:311827-311947 1.0000 120 chr2L:5240343-5240463 1.0000 120 chrX:11794400-11794520 1.0000 120 chr3L:10526104-10526224 1.0000 120 chr3L:21402859-21402979 1.0000 120 chr3L:4531635-4531755 1.0000 120 chrX:13563175-13563295 1.0000 120 chr2R:16216368-16216488 1.0000 120 chr3L:11250586-11250706 1.0000 120 chr3L:627496-627616 1.0000 120 chr2L:3426443-3426563 1.0000 120 chr2L:8291796-8291916 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_eve/ -dna -nmotifs 5 -w 8 -maxsize 250000 -nostatus ../result/final_prediction/fly/fasta/RankLinear8.0_60/eve.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 0.317 C 0.185 G 0.179 T 0.318 Background letter frequencies (from file dataset with add-one prior applied): A 0.317 C 0.185 G 0.179 T 0.318 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF GGGTCAGC MEME-1 width = 8 sites = 8 llr = 90 E-value = 1.9e+003 ******************************************************************************** -------------------------------------------------------------------------------- Motif GGGTCAGC MEME-1 Description -------------------------------------------------------------------------------- Simplified A ::::39:: pos.-specific C ::::8::a probability G aaa1:1a: matrix T :::9:::: bits 2.5 *** ** 2.2 *** ** 2.0 *** ** 1.7 *** ** Relative 1.5 *** * ** Entropy 1.2 ******** (16.2 bits) 1.0 ******** 0.7 ******** 0.5 ******** 0.2 ******** 0.0 -------- Multilevel GGGTCAGC consensus A sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGGTCAGC MEME-1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr3R:5279326-5279446 11 3.54e-06 ACTTCAACGA GGGTCAGC AGTCAGTCCC chr2R:13582390-13582510 87 3.54e-06 AGGTCTTGCT GGGTCAGC TTTATGGCTG chr2L:21316881-21317001 53 3.54e-06 AGTTGTCGCT GGGTCAGC TTTTACAAGA chr3L:551986-552106 12 3.54e-06 ATGGTGGATG GGGTCAGC TAGTCGAGGC chr3L:16689669-16689789 74 7.54e-06 AAGCCAGGGA GGGGCAGC AGTTACGACT chr3R:9885352-9885472 73 7.54e-06 ATGACATAAA GGGTCGGC AAGGAATCCT chr3L:10844203-10844323 62 1.36e-05 TCATTTTACT GGGTAAGC AGTTCGAGTT chr3R:26954878-26954998 21 1.36e-05 TGGTTACCAT GGGTAAGC TTGACTGTCA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGGTCAGC MEME-1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr3R:5279326-5279446 3.5e-06 10_[+1]_102 chr2R:13582390-13582510 3.5e-06 86_[+1]_26 chr2L:21316881-21317001 3.5e-06 52_[+1]_60 chr3L:551986-552106 3.5e-06 11_[+1]_101 chr3L:16689669-16689789 7.5e-06 73_[+1]_39 chr3R:9885352-9885472 7.5e-06 72_[+1]_40 chr3L:10844203-10844323 1.4e-05 61_[+1]_51 chr3R:26954878-26954998 1.4e-05 20_[+1]_92 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGGTCAGC MEME-1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF GGGTCAGC width=8 seqs=8 chr3R:5279326-5279446 ( 11) GGGTCAGC 1 chr2R:13582390-13582510 ( 87) GGGTCAGC 1 chr2L:21316881-21317001 ( 53) GGGTCAGC 1 chr3L:551986-552106 ( 12) GGGTCAGC 1 chr3L:16689669-16689789 ( 74) GGGGCAGC 1 chr3R:9885352-9885472 ( 73) GGGTCGGC 1 chr3L:10844203-10844323 ( 62) GGGTAAGC 1 chr3R:26954878-26954998 ( 21) GGGTAAGC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGGTCAGC MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 28250 bayes= 12.5227 E= 1.9e+003 -965 -965 248 -965 -965 -965 248 -965 -965 -965 248 -965 -965 -965 -52 146 -34 202 -965 -965 146 -965 -52 -965 -965 -965 248 -965 -965 243 -965 -965 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGGTCAGC MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 8 E= 1.9e+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 0.125000 0.875000 0.250000 0.750000 0.000000 0.000000 0.875000 0.000000 0.125000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGGTCAGC MEME-1 regular expression -------------------------------------------------------------------------------- GGGT[CA]AGC -------------------------------------------------------------------------------- Time 8.70 secs. ******************************************************************************** ******************************************************************************** MOTIF CTGCCGCC MEME-2 width = 8 sites = 3 llr = 39 E-value = 2.6e+004 ******************************************************************************** -------------------------------------------------------------------------------- Motif CTGCCGCC MEME-2 Description -------------------------------------------------------------------------------- Simplified A :::::::: pos.-specific C a::aa:aa probability G ::a::a:: matrix T :a:::::: bits 2.5 * ****** 2.2 * ****** 2.0 * ****** 1.7 ******** Relative 1.5 ******** Entropy 1.2 ******** (18.8 bits) 1.0 ******** 0.7 ******** 0.5 ******** 0.2 ******** 0.0 -------- Multilevel CTGCCGCC consensus sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTGCCGCC MEME-2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr3L:21048730-21048850 9 2.21e-06 CAGCTACA CTGCCGCC CAGTATTACA chr2R:12539186-12539306 42 2.21e-06 CAACTGTTCT CTGCCGCC TAACTTATAA chr3L:9124620-9124740 64 2.21e-06 AAAATCCAAA CTGCCGCC TTGTGAGCCC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTGCCGCC MEME-2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr3L:21048730-21048850 2.2e-06 8_[+2]_104 chr2R:12539186-12539306 2.2e-06 41_[+2]_71 chr3L:9124620-9124740 2.2e-06 63_[+2]_49 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTGCCGCC MEME-2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF CTGCCGCC width=8 seqs=3 chr3L:21048730-21048850 ( 9) CTGCCGCC 1 chr2R:12539186-12539306 ( 42) CTGCCGCC 1 chr3L:9124620-9124740 ( 64) CTGCCGCC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTGCCGCC MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 28250 bayes= 12.8598 E= 2.6e+004 -823 243 -823 -823 -823 -823 -823 165 -823 -823 248 -823 -823 243 -823 -823 -823 243 -823 -823 -823 -823 248 -823 -823 243 -823 -823 -823 243 -823 -823 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTGCCGCC MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 3 E= 2.6e+004 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 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTGCCGCC MEME-2 regular expression -------------------------------------------------------------------------------- CTGCCGCC -------------------------------------------------------------------------------- Time 15.03 secs. ******************************************************************************** ******************************************************************************** MOTIF CGBGGGCG MEME-3 width = 8 sites = 3 llr = 37 E-value = 3.8e+004 ******************************************************************************** -------------------------------------------------------------------------------- Motif CGBGGGCG MEME-3 Description -------------------------------------------------------------------------------- Simplified A :::::::: pos.-specific C a:3:::a: probability G :a3aaa:a matrix T ::3::::: bits 2.5 ** ***** 2.2 ** ***** 2.0 ** ***** 1.7 ** ***** Relative 1.5 ** ***** Entropy 1.2 ** ***** (17.9 bits) 1.0 ** ***** 0.7 ** ***** 0.5 ******** 0.2 ******** 0.0 -------- Multilevel CGCGGGCG consensus G sequence T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CGBGGGCG MEME-3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr3R:25515165-25515285 32 2.29e-06 TTGAATTTTG CGGGGGCG TGCCGACATT chr2R:16716341-16716461 15 2.29e-06 ATATGTTTGT CGCGGGCG TATTCATTTC chr3R:5020820-5020940 27 4.29e-06 TTATGTATGC CGTGGGCG AGTGTTACAT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CGBGGGCG MEME-3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr3R:25515165-25515285 2.3e-06 31_[+3]_81 chr2R:16716341-16716461 2.3e-06 14_[+3]_98 chr3R:5020820-5020940 4.3e-06 26_[+3]_86 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CGBGGGCG MEME-3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF CGBGGGCG width=8 seqs=3 chr3R:25515165-25515285 ( 32) CGGGGGCG 1 chr2R:16716341-16716461 ( 15) CGCGGGCG 1 chr3R:5020820-5020940 ( 27) CGTGGGCG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CGBGGGCG MEME-3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 28250 bayes= 13.6483 E= 3.8e+004 -823 243 -823 -823 -823 -823 248 -823 -823 84 89 7 -823 -823 248 -823 -823 -823 248 -823 -823 -823 248 -823 -823 243 -823 -823 -823 -823 248 -823 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CGBGGGCG MEME-3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 3 E= 3.8e+004 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.333333 0.333333 0.333333 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 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CGBGGGCG MEME-3 regular expression -------------------------------------------------------------------------------- CG[CGT]GGGCG -------------------------------------------------------------------------------- Time 21.40 secs. ******************************************************************************** ******************************************************************************** MOTIF GTGGGKGG MEME-4 width = 8 sites = 2 llr = 24 E-value = 5.4e+004 ******************************************************************************** -------------------------------------------------------------------------------- Motif GTGGGKGG MEME-4 Description -------------------------------------------------------------------------------- Simplified A :::::::: pos.-specific C :::::::: probability G a:aaa5aa matrix T :a:::5:: bits 2.5 * *** ** 2.2 * *** ** 2.0 * *** ** 1.7 ***** ** Relative 1.5 ***** ** Entropy 1.2 ***** ** (17.6 bits) 1.0 ******** 0.7 ******** 0.5 ******** 0.2 ******** 0.0 -------- Multilevel GTGGGGGG consensus T sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GTGGGKGG MEME-4 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr3L:10844203-10844323 44 1.87e-06 TTTAATAGTT GTGGGGGG TCATTTTACT chrX:17477136-17477256 67 5.20e-06 AAATGTAACA GTGGGTGG TGGCTGATTT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GTGGGKGG MEME-4 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr3L:10844203-10844323 1.9e-06 43_[+4]_69 chrX:17477136-17477256 5.2e-06 66_[+4]_46 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GTGGGKGG MEME-4 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF GTGGGKGG width=8 seqs=2 chr3L:10844203-10844323 ( 44) GTGGGGGG 1 chrX:17477136-17477256 ( 67) GTGGGTGG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GTGGGKGG MEME-4 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 28250 bayes= 12.9378 E= 5.4e+004 -765 -765 247 -765 -765 -765 -765 165 -765 -765 247 -765 -765 -765 247 -765 -765 -765 247 -765 -765 -765 148 65 -765 -765 247 -765 -765 -765 247 -765 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GTGGGKGG MEME-4 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 2 E= 5.4e+004 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 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 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GTGGGKGG MEME-4 regular expression -------------------------------------------------------------------------------- GTGGG[GT]GG -------------------------------------------------------------------------------- Time 27.71 secs. ******************************************************************************** ******************************************************************************** MOTIF GGCTTGGS MEME-5 width = 8 sites = 3 llr = 36 E-value = 2.0e+005 ******************************************************************************** -------------------------------------------------------------------------------- Motif GGCTTGGS MEME-5 Description -------------------------------------------------------------------------------- Simplified A :::::::: pos.-specific C ::a::::7 probability G aa:::aa3 matrix T :::aa::: bits 2.5 *** ** 2.2 *** ** 2.0 *** ** 1.7 ******* Relative 1.5 ******** Entropy 1.2 ******** (17.2 bits) 1.0 ******** 0.7 ******** 0.5 ******** 0.2 ******** 0.0 -------- Multilevel GGCTTGGC consensus G sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGCTTGGS MEME-5 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chrX:11794400-11794520 58 3.55e-06 TTAATTGTCT GGCTTGGC TTGCCCTAGT chr2L:14409084-14409204 63 3.55e-06 TTATTTCTTT GGCTTGGC CGTTTTTGGT chr2R:16833365-16833485 55 6.99e-06 GCACACCTTC GGCTTGGG CTCCCAAGTA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGCTTGGS MEME-5 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrX:11794400-11794520 3.6e-06 57_[+5]_55 chr2L:14409084-14409204 3.6e-06 62_[+5]_50 chr2R:16833365-16833485 7e-06 54_[+5]_58 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGCTTGGS MEME-5 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF GGCTTGGS width=8 seqs=3 chrX:11794400-11794520 ( 58) GGCTTGGC 1 chr2L:14409084-14409204 ( 63) GGCTTGGC 1 chr2R:16833365-16833485 ( 55) GGCTTGGG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGCTTGGS MEME-5 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 28250 bayes= 13.6483 E= 2.0e+005 -823 -823 248 -823 -823 -823 248 -823 -823 243 -823 -823 -823 -823 -823 165 -823 -823 -823 165 -823 -823 248 -823 -823 -823 248 -823 -823 184 89 -823 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGCTTGGS MEME-5 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 3 E= 2.0e+005 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 0.000000 1.000000 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 0.666667 0.333333 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGCTTGGS MEME-5 regular expression -------------------------------------------------------------------------------- GGCTTGG[CG] -------------------------------------------------------------------------------- Time 34.28 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrX:3688731-3688851 4.56e-01 120 chr3L:9114894-9115014 7.03e-01 120 chr2L:11970496-11970616 9.99e-01 120 chr2R:22401171-22401291 6.38e-01 120 chr3R:9337246-9337366 7.70e-01 120 chr2R:9556986-9557106 7.84e-01 120 chr2L:14536480-14536600 8.74e-01 120 chr2R:5662409-5662529 8.46e-01 120 chr3R:29254921-29255041 2.70e-02 71_[+3(7.89e-05)]_41 chr2R:15909120-15909240 9.99e-01 120 chr3R:26954878-26954998 2.11e-02 20_[+1(1.36e-05)]_92 chr2L:14409084-14409204 6.50e-04 62_[+5(3.55e-06)]_50 chr3R:21061178-21061298 3.22e-02 120 chr3R:6425072-6425192 3.99e-01 120 chr2R:11666059-11666179 9.76e-01 120 chr3R:9442123-9442243 9.68e-01 120 chr4:559596-559716 6.15e-01 120 chrX:6864713-6864833 5.77e-01 120 chr2R:23581536-23581656 8.94e-01 120 chr2L:20803197-20803317 1.00e+00 120 chr2R:9550649-9550769 4.39e-01 120 chr3L:12487745-12487865 1.03e-03 1_[+4(7.30e-05)]_111 chrX:13375145-13375265 9.09e-01 120 chr3L:17486534-17486654 9.99e-01 120 chr2L:8091603-8091723 9.63e-01 120 chr3R:19001425-19001545 1.18e-01 120 chr3R:21058882-21059002 8.42e-01 120 chr3L:21014076-21014196 1.00e+00 120 chr2L:1446194-1446314 8.35e-02 120 chr3L:614365-614485 8.96e-02 120 chr2L:1461355-1461475 1.88e-01 120 chr3L:346121-346241 2.10e-01 120 chr3L:6695476-6695596 6.38e-01 120 chr3L:22362752-22362872 5.06e-01 120 chr2R:10517489-10517609 9.88e-01 120 chr3L:21045516-21045636 8.41e-02 120 chr2L:14477331-14477451 9.27e-01 120 chr3L:551986-552106 1.03e-03 11_[+1(3.54e-06)]_101 chr2L:2732197-2732317 3.52e-02 120 chr3L:9124620-9124740 2.26e-02 63_[+2(2.21e-06)]_49 chr2L:1737820-1737940 3.30e-01 120 chr3L:10844203-10844323 1.74e-04 43_[+4(1.87e-06)]_10_[+1(1.36e-05)]_\ 51 chr2L:10590363-10590483 1.73e-02 74_[+4(7.30e-05)]_38 chr2R:16617206-16617326 9.82e-01 120 chr3R:14034776-14034896 1.97e-04 61_[+4(1.04e-05)]_51 chrX:15893602-15893722 8.99e-01 120 chrX:2362852-2362972 9.59e-01 120 chr3R:10601630-10601750 7.38e-01 120 chrX:15631130-15631250 4.03e-02 120 chr2R:12258833-12258953 1.00e+00 120 chr2R:13925093-13925213 7.38e-01 120 chr2R:19270588-19270708 1.97e-01 120 chrX:5417555-5417675 6.27e-01 120 chr3R:14740262-14740382 9.94e-01 120 chr2R:7746098-7746218 9.96e-01 120 chr2L:312110-312230 9.61e-01 120 chr2R:16716341-16716461 4.80e-03 14_[+3(2.29e-06)]_98 chrX:19165807-19165927 5.34e-01 120 chr2R:15898667-15898787 1.56e-01 120 chr3L:469022-469142 9.93e-01 120 chr3R:19322536-19322656 3.03e-01 120 chr2L:3713650-3713770 5.62e-01 120 chr2L:225739-225859 8.35e-01 120 chr2R:11603998-11604118 9.36e-01 120 chr3R:9885352-9885472 1.68e-02 72_[+1(7.54e-06)]_40 chr3L:7787517-7787637 7.86e-01 120 chr2L:3144385-3144505 1.72e-01 120 chr2L:482956-483076 9.99e-01 120 chr3L:8553794-8553914 9.67e-01 120 chr2L:2854901-2855021 7.15e-01 120 chr2R:19803893-19804013 7.62e-01 120 chr3R:13997465-13997585 9.43e-01 120 chr2R:5987973-5988093 8.21e-01 120 chr2R:12736968-12737088 9.83e-01 120 chr4:66810-66930 9.36e-01 120 chr3R:6474954-6475074 4.07e-01 120 chr2L:18319380-18319500 9.99e-01 120 chr2R:11658719-11658839 7.96e-01 120 chr3R:17055874-17055994 3.15e-01 51_[+4(7.30e-05)]_61 chr3L:3383579-3383699 8.84e-01 120 chr2R:5992442-5992562 9.57e-01 120 chr2L:1657780-1657900 9.79e-01 120 chr2L:3146030-3146150 9.79e-01 120 chr3L:632748-632868 7.15e-01 120 chr2R:6117179-6117299 3.68e-01 120 chr3R:25515165-25515285 7.41e-05 31_[+3(2.29e-06)]_81 chr3L:18030546-18030666 7.85e-01 120 chr3L:15698821-15698941 2.56e-01 120 chr2R:11650423-11650543 1.00e+00 120 chr3R:27149581-27149701 4.56e-01 120 chr3R:9502910-9503030 1.00e+00 120 chr3L:19019900-19020020 6.42e-01 120 chr3L:4121719-4121839 8.83e-01 120 chr3L:491294-491414 8.18e-01 120 chr3R:30815589-30815709 1.00e+00 120 chr2R:19167872-19167992 6.92e-01 120 chrX:18358481-18358601 1.73e-01 120 chr2L:16633644-16633764 8.99e-01 120 chr3L:3072856-3072976 7.19e-01 120 chr2R:25226927-25227047 1.00e+00 120 chr2R:11712524-11712644 9.36e-01 120 chr2L:18320635-18320755 5.86e-01 120 chr3L:18757694-18757814 9.82e-01 120 chr3R:13998308-13998428 8.90e-01 120 chr2R:8052322-8052442 9.24e-01 120 chr2R:18355167-18355287 3.52e-01 120 chr3L:473551-473671 2.52e-01 120 chr3R:21657857-21657977 9.14e-01 120 chr2L:1213744-1213864 9.28e-01 120 chr3L:1580857-1580977 1.99e-01 120 chr3L:10681378-10681498 5.77e-02 120 chr3R:10267733-10267853 4.77e-01 120 chr2R:16717501-16717621 8.35e-01 120 chr2R:6964282-6964402 1.00e+00 120 chr2R:13540453-13540573 1.15e-01 120 chrX:9551346-9551466 2.44e-01 120 chr2R:12539186-12539306 3.66e-03 41_[+2(2.21e-06)]_71 chr2L:16545307-16545427 3.91e-01 120 chr3R:21659226-21659346 8.20e-01 120 chr2R:9309135-9309255 7.32e-01 120 chr2L:3100093-3100213 9.55e-01 120 chr2R:9549186-9549306 9.94e-01 120 chr3R:30782393-30782513 7.67e-01 120 chrX:1964577-1964697 9.95e-01 120 chr3R:9877297-9877417 9.45e-01 120 chr3L:19565197-19565317 4.65e-01 120 chr3L:4347583-4347703 6.98e-01 120 chr3R:5075221-5075341 1.19e-01 120 chr2L:1642609-1642729 9.96e-01 120 chr3R:14019100-14019220 9.30e-01 120 chr2L:511297-511417 4.50e-01 120 chr3R:23220969-23221089 8.19e-01 120 chr2L:55569-55689 5.29e-01 120 chrX:12574249-12574369 3.96e-01 120 chr2R:5495614-5495734 2.70e-01 120 chr3L:11488150-11488270 3.16e-01 120 chr2L:8735332-8735452 9.54e-01 120 chr2R:6159576-6159696 7.01e-01 120 chr3L:17488034-17488154 3.91e-01 120 chr2R:19415975-19416095 8.08e-01 120 chrX:3749262-3749382 1.00e+00 120 chr3L:8952109-8952229 3.69e-01 103_[+2(7.57e-05)]_9 chr2L:13059662-13059782 5.12e-01 120 chr4:1038824-1038944 9.99e-01 120 chr2R:16833365-16833485 4.63e-02 54_[+5(6.99e-06)]_58 chr3L:1570737-1570857 5.28e-01 120 chr4:957759-957879 1.95e-02 70_[+3(7.89e-05)]_42 chr3R:9535344-9535464 3.31e-01 120 chr2L:491702-491822 9.82e-01 120 chr3R:10392529-10392649 5.92e-01 120 chr2L:14198514-14198634 4.42e-01 120 chr3R:24602355-24602475 6.22e-01 120 chr4:1009436-1009556 9.36e-01 120 chrX:688338-688458 8.05e-01 120 chr3R:17402103-17402223 7.64e-01 120 chr3R:11605176-11605296 9.92e-01 120 chr3L:13113658-13113778 4.66e-02 27_[+2(7.57e-05)]_85 chr2L:1653907-1654027 9.90e-01 120 chr3R:32032962-32033082 1.00e+00 120 chrX:18919564-18919684 9.21e-01 120 chrX:17477136-17477256 9.98e-03 66_[+4(5.20e-06)]_46 chr2L:159533-159653 3.82e-01 120 chr3R:21298367-21298487 1.00e+00 120 chr4:553280-553400 8.34e-01 120 chr2L:4996653-4996773 3.15e-01 120 chr2L:11060053-11060173 8.18e-01 120 chr2L:162440-162560 8.01e-01 120 chr4:155799-155919 3.71e-01 120 chr3R:16279637-16279757 8.72e-01 120 chr2L:21316881-21317001 4.93e-03 52_[+1(3.54e-06)]_60 chr2L:2897873-2897993 6.38e-02 120 chr2L:9704882-9705002 1.65e-01 120 chr3R:10033095-10033215 5.53e-01 120 chr2R:12955524-12955644 1.39e-01 120 chr3R:17944423-17944543 9.17e-01 120 chr2R:15891611-15891731 5.38e-01 120 chr3L:2546472-2546592 3.50e-01 120 chr2R:13582390-13582510 4.74e-03 86_[+1(3.54e-06)]_26 chr3L:12565555-12565675 1.00e+00 120 chr2L:20860223-20860343 4.97e-01 120 chr2L:16619044-16619164 9.98e-01 120 chr3R:9548515-9548635 8.95e-01 120 chr3R:20956359-20956479 8.97e-01 120 chr2R:7785350-7785470 6.42e-01 120 chr3L:8006387-8006507 2.29e-01 120 chr3R:5122287-5122407 9.89e-01 120 chrX:10513809-10513929 9.98e-01 120 chr3R:9446949-9447069 8.44e-01 120 chr3L:131004-131124 1.40e-01 120 chr3R:14059192-14059312 4.45e-01 120 chr3R:10276287-10276407 1.77e-01 120 chr4:833580-833700 5.95e-01 120 chr2R:25030563-25030683 4.46e-01 120 chr3R:5020820-5020940 1.31e-04 26_[+3(4.29e-06)]_86 chr3R:5037808-5037928 8.14e-01 120 chr3R:15122659-15122779 9.40e-01 120 chrX:14211889-14212009 6.42e-01 120 chr3L:3786532-3786652 1.17e-01 120 chr3L:21048730-21048850 2.42e-03 8_[+2(2.21e-06)]_104 chr3R:11762217-11762337 9.39e-01 120 chr2R:9668388-9668508 4.90e-01 120 chr3L:8832228-8832348 4.67e-01 120 chr3L:13114619-13114739 9.99e-01 120 chrX:19602148-19602268 9.99e-01 120 chr3R:10590527-10590647 1.64e-01 120 chr3R:29457898-29458018 6.75e-02 120 chr3R:30565979-30566099 9.92e-01 120 chr3L:2585142-2585262 6.88e-02 120 chr2R:6142019-6142139 7.52e-01 120 chr3R:15666487-15666607 4.36e-02 120 chr2R:5362447-5362567 6.40e-01 120 chr2L:8559067-8559187 3.38e-02 45_[+3(7.89e-05)]_67 chr2R:10480931-10481051 7.00e-01 120 chr3R:23174208-23174328 7.81e-01 120 chr3L:4310711-4310831 4.84e-01 120 chr3L:5975612-5975732 3.05e-01 120 chr2L:18643649-18643769 7.17e-01 120 chr3R:9419817-9419937 9.79e-01 120 chr3L:2457203-2457323 8.61e-01 120 chr2R:17116656-17116776 9.97e-01 120 chr2R:7759490-7759610 3.57e-01 120 chr2L:5869276-5869396 2.00e-01 120 chr2R:5704319-5704439 1.16e-01 120 chr3R:13363870-13363990 9.18e-01 120 chr2R:25008390-25008510 9.93e-01 120 chr3L:22199509-22199629 3.12e-01 120 chr3L:4607186-4607306 3.12e-01 120 chr2L:10241116-10241236 4.66e-01 120 chrX:6872420-6872540 1.92e-01 31_[+2(7.57e-05)]_81 chr2R:10526262-10526382 9.83e-01 120 chr3L:16689669-16689789 4.77e-03 73_[+1(7.54e-06)]_39 chr3R:14289703-14289823 8.51e-01 120 chr3L:16985250-16985370 9.15e-02 120 chr3R:5279326-5279446 4.48e-03 10_[+1(3.54e-06)]_102 chr2L:16353886-16354006 1.88e-01 120 chr2R:7757642-7757762 9.92e-01 120 chr3L:11254951-11255071 1.39e-01 120 chrX:3751507-3751627 7.60e-01 120 chr4:311827-311947 7.01e-02 120 chr2L:5240343-5240463 4.04e-01 120 chrX:11794400-11794520 3.59e-02 57_[+5(3.55e-06)]_55 chr3L:10526104-10526224 9.78e-01 120 chr3L:21402859-21402979 8.36e-01 120 chr3L:4531635-4531755 6.37e-01 120 chrX:13563175-13563295 8.32e-01 120 chr2R:16216368-16216488 2.73e-01 120 chr3L:11250586-11250706 5.32e-02 120 chr3L:627496-627616 5.99e-01 120 chr2L:3426443-3426563 9.35e-01 120 chr2L:8291796-8291916 9.47e-01 120 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (5) found. ******************************************************************************** CPU: c28n03.farnam.hpc.yale.internal ********************************************************************************