******************************************************************************** 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/CG14655.fasta CONTROL SEQUENCES= --none-- ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ chr3R:18486302-18486422 1.0000 120 chr3R:18491264-18491384 1.0000 120 chrX:9654071-9654191 1.0000 120 chr3R:12315569-12315689 1.0000 120 chr3L:2162774-2162894 1.0000 120 chr3L:17045808-17045928 1.0000 120 chr3L:21224452-21224572 1.0000 120 chr3R:10531949-10532069 1.0000 120 chr3L:18231576-18231696 1.0000 120 chr3R:29211876-29211996 1.0000 120 chr2L:734268-734388 1.0000 120 chr3R:19788904-19789024 1.0000 120 chr3L:4271577-4271697 1.0000 120 chr2L:4622064-4622184 1.0000 120 chr2L:20328753-20328873 1.0000 120 chr3L:14483126-14483246 1.0000 120 chr3L:5626613-5626733 1.0000 120 chr2R:18656795-18656915 1.0000 120 chr3R:23392367-23392487 1.0000 120 chr2R:7114733-7114853 1.0000 120 chr3R:26894035-26894155 1.0000 120 chr3L:1484881-1485001 1.0000 120 chr2L:14260001-14260121 1.0000 120 chr3R:21906985-21907105 1.0000 120 chr3L:17504723-17504843 1.0000 120 chr3L:3536539-3536659 1.0000 120 chr2R:14119316-14119436 1.0000 120 chr3L:18096882-18097002 1.0000 120 chrX:7637273-7637393 1.0000 120 chr2L:7513819-7513939 1.0000 120 chr3R:18488020-18488140 1.0000 120 chrX:13951549-13951669 1.0000 120 chr3R:10842538-10842658 1.0000 120 chr3L:14440735-14440855 1.0000 120 chr2R:7112254-7112374 1.0000 120 chr2L:4633157-4633277 1.0000 120 chr3R:22576218-22576338 1.0000 120 chr3L:4398048-4398168 1.0000 120 chr2L:4648941-4649061 1.0000 120 chr2R:12736677-12736797 1.0000 120 chrX:4963114-4963234 1.0000 120 chr3L:3555238-3555358 1.0000 120 chrX:15639168-15639288 1.0000 120 chr3R:18492058-18492178 1.0000 120 chr2R:22727164-22727284 1.0000 120 chr2R:13291883-13292003 1.0000 120 chrX:5924527-5924647 1.0000 120 chr2L:18752933-18753053 1.0000 120 chr3L:3791225-3791345 1.0000 120 chr2R:17496980-17497100 1.0000 120 chr2R:14083090-14083210 1.0000 120 chrX:10539243-10539363 1.0000 120 chr3R:31767652-31767772 1.0000 120 chr3L:9765337-9765457 1.0000 120 chr3L:12073247-12073367 1.0000 120 chr3R:8788028-8788148 1.0000 120 chr3R:31944356-31944476 1.0000 120 chr3L:4745278-4745398 1.0000 120 chr2R:15233472-15233592 1.0000 120 chr3R:25451960-25452080 1.0000 120 chr3R:25644323-25644443 1.0000 120 chr2R:15599991-15600111 1.0000 120 chr2R:12739826-12739946 1.0000 120 chr3R:22400391-22400511 1.0000 120 chr3L:9745541-9745661 1.0000 120 chrX:4170623-4170743 1.0000 120 chr3L:18245930-18246050 1.0000 120 chr2L:4635521-4635641 1.0000 120 chr3L:10903547-10903667 1.0000 120 chr3L:22106841-22106961 1.0000 120 chr2L:684910-685030 1.0000 120 chr2L:1538253-1538373 1.0000 120 chr2L:18744015-18744135 1.0000 120 chr3R:26478169-26478289 1.0000 120 chr2R:21783562-21783682 1.0000 120 chr3L:485494-485614 1.0000 120 chrX:838117-838237 1.0000 120 chr2R:7161980-7162100 1.0000 120 chr2R:21801104-21801224 1.0000 120 chr3R:18499458-18499578 1.0000 120 chr3L:6355162-6355282 1.0000 120 chrX:17686390-17686510 1.0000 120 chr2R:20143495-20143615 1.0000 120 chr2L:14413495-14413615 1.0000 120 chrX:724617-724737 1.0000 120 chrX:8747802-8747922 1.0000 120 chrX:5014793-5014913 1.0000 120 chr3L:16454657-16454777 1.0000 120 chr2R:12413294-12413414 1.0000 120 chr2L:18348779-18348899 1.0000 120 chr2R:12720724-12720844 1.0000 120 chr2R:20057880-20058000 1.0000 120 chr2R:19904084-19904204 1.0000 120 chr2L:7627601-7627721 1.0000 120 chr2R:10847409-10847529 1.0000 120 chr3L:16454440-16454560 1.0000 120 chrX:18800298-18800418 1.0000 120 chr3R:19383455-19383575 1.0000 120 chr3R:17814317-17814437 1.0000 120 chr3R:22158372-22158492 1.0000 120 chr3R:4957936-4958056 1.0000 120 chr3R:11945606-11945726 1.0000 120 chr3L:15187917-15188037 1.0000 120 chrX:378443-378563 1.0000 120 chrX:15156410-15156530 1.0000 120 chr2L:661080-661200 1.0000 120 chr3L:5945719-5945839 1.0000 120 chr3L:21223425-21223545 1.0000 120 chr2R:6869570-6869690 1.0000 120 chr2R:8319977-8320097 1.0000 120 chr3R:18485390-18485510 1.0000 120 chr2L:18746853-18746973 1.0000 120 chr3R:30344676-30344796 1.0000 120 chr2R:8596670-8596790 1.0000 120 chr2R:16706829-16706949 1.0000 120 chr3R:31314607-31314727 1.0000 120 chr2L:653936-654056 1.0000 120 chr2L:20840207-20840327 1.0000 120 chr3R:21979513-21979633 1.0000 120 chr3L:18245097-18245217 1.0000 120 chr3R:27181259-27181379 1.0000 120 chr3L:14616735-14616855 1.0000 120 chr3L:21237127-21237247 1.0000 120 chr3R:26479373-26479493 1.0000 120 chrX:8839530-8839650 1.0000 120 chr2R:20196898-20197018 1.0000 120 chrX:5013180-5013300 1.0000 120 chrX:8163581-8163701 1.0000 120 chrX:2796728-2796848 1.0000 120 chr3R:15113722-15113842 1.0000 120 chr3L:20988009-20988129 1.0000 120 chr3L:16019259-16019379 1.0000 120 chr2L:19936244-19936364 1.0000 120 chr3R:30872814-30872934 1.0000 120 chr3R:24024270-24024390 1.0000 120 chr2L:15474512-15474632 1.0000 120 chrX:5038586-5038706 1.0000 120 chr2L:4797732-4797852 1.0000 120 chr3L:12072522-12072642 1.0000 120 chr3L:20983459-20983579 1.0000 120 chr2L:3645476-3645596 1.0000 120 chrX:11736554-11736674 1.0000 120 chr3L:17981240-17981360 1.0000 120 chr2L:18752169-18752289 1.0000 120 chr3R:9480578-9480698 1.0000 120 chr3L:18076754-18076874 1.0000 120 chr2R:18663211-18663331 1.0000 120 chr2R:11315581-11315701 1.0000 120 chr3R:19070765-19070885 1.0000 120 chr3L:8319238-8319358 1.0000 120 chr3L:6308750-6308870 1.0000 120 chr2R:18569195-18569315 1.0000 120 chr3L:18248536-18248656 1.0000 120 chr2R:23198704-23198824 1.0000 120 chr3L:16751788-16751908 1.0000 120 chr2R:16710942-16711062 1.0000 120 chr3L:6396024-6396144 1.0000 120 chr3L:7632978-7633098 1.0000 120 chrX:4959037-4959157 1.0000 120 chr3R:11616392-11616512 1.0000 120 chr2R:20055395-20055515 1.0000 120 chr2R:7622148-7622268 1.0000 120 chr3L:22192354-22192474 1.0000 120 chrX:18558756-18558876 1.0000 120 chr3L:12109367-12109487 1.0000 120 chr2R:18353624-18353744 1.0000 120 chr2R:6521299-6521419 1.0000 120 chr3L:6307414-6307534 1.0000 120 chr2R:17243852-17243972 1.0000 120 chr3R:7025388-7025508 1.0000 120 chr2L:19317945-19318065 1.0000 120 chr2R:20568436-20568556 1.0000 120 chr2L:20328077-20328197 1.0000 120 chrX:3739278-3739398 1.0000 120 chrX:17112145-17112265 1.0000 120 chrX:23071347-23071467 1.0000 120 chr2L:20335071-20335191 1.0000 120 chr2R:8596870-8596990 1.0000 120 chr3L:14462481-14462601 1.0000 120 chr3R:13797456-13797576 1.0000 120 chr3R:31712700-31712820 1.0000 120 chr3R:13875545-13875665 1.0000 120 chr3L:767066-767186 1.0000 120 chr3L:2486626-2486746 1.0000 120 chr3L:4393014-4393134 1.0000 120 chr2L:20340761-20340881 1.0000 120 chr3L:9209252-9209372 1.0000 120 chr3L:4346472-4346592 1.0000 120 chr2R:23306111-23306231 1.0000 120 chr3R:30567365-30567485 1.0000 120 chr3L:741832-741952 1.0000 120 chr3R:19075275-19075395 1.0000 120 chr2L:5495097-5495217 1.0000 120 chr3R:14720227-14720347 1.0000 120 chrX:4999142-4999262 1.0000 120 chr3L:9765537-9765657 1.0000 120 chr3L:4336683-4336803 1.0000 120 chr2R:8645858-8645978 1.0000 120 chrX:14922538-14922658 1.0000 120 chr3R:27685594-27685714 1.0000 120 chr2R:21531619-21531739 1.0000 120 chr3R:29072965-29073085 1.0000 120 chrX:6745683-6745803 1.0000 120 chr2L:21246812-21246932 1.0000 120 chr3L:16464079-16464199 1.0000 120 chr3L:10396693-10396813 1.0000 120 chr2L:20370278-20370398 1.0000 120 chr3L:14422303-14422423 1.0000 120 chr2R:17077070-17077190 1.0000 120 chr3R:30312636-30312756 1.0000 120 chrX:9738618-9738738 1.0000 120 chr2R:17811086-17811206 1.0000 120 chr3R:14280486-14280606 1.0000 120 chr2R:12534446-12534566 1.0000 120 chr3L:590009-590129 1.0000 120 chr3L:20914560-20914680 1.0000 120 chrX:11544702-11544822 1.0000 120 chr2L:19574574-19574694 1.0000 120 chr2R:21377333-21377453 1.0000 120 chr2L:16281790-16281910 1.0000 120 chr3R:26019349-26019469 1.0000 120 chr2R:14081668-14081788 1.0000 120 chr3R:15567109-15567229 1.0000 120 chr2R:21550607-21550727 1.0000 120 chr3L:9209049-9209169 1.0000 120 chr3L:6266238-6266358 1.0000 120 chr3R:22594398-22594518 1.0000 120 chrX:293439-293559 1.0000 120 chr2L:20721590-20721710 1.0000 120 chr3R:22150084-22150204 1.0000 120 chrX:15123567-15123687 1.0000 120 chrX:17914639-17914759 1.0000 120 chr3L:18248852-18248972 1.0000 120 chr2R:5781960-5782080 1.0000 120 chr3R:4687363-4687483 1.0000 120 chr2R:14317129-14317249 1.0000 120 chr2R:22142236-22142356 1.0000 120 chr3R:19074399-19074519 1.0000 120 chr3L:2533150-2533270 1.0000 120 chr3R:21895992-21896112 1.0000 120 chr2R:16212935-16213055 1.0000 120 chr3R:19255371-19255491 1.0000 120 chr3R:6214371-6214491 1.0000 120 chrX:19173107-19173227 1.0000 120 chr3L:14145782-14145902 1.0000 120 chr3L:11444279-11444399 1.0000 120 chr2L:1388008-1388128 1.0000 120 chr2R:8646570-8646690 1.0000 120 chr2L:4065326-4065446 1.0000 120 chr2L:7971523-7971643 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_CG14655/ -dna -nmotifs 5 -w 8 -maxsize 250000 -nostatus ../result/final_prediction/fly/fasta/RankLinear8.0_60/CG14655.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 0.352 C 0.152 G 0.148 T 0.348 Background letter frequencies (from file dataset with add-one prior applied): A 0.352 C 0.152 G 0.148 T 0.348 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF GTGCACWG MEME-1 width = 8 sites = 8 llr = 96 E-value = 2.7e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif GTGCACWG MEME-1 Description -------------------------------------------------------------------------------- Simplified A ::::a:5: pos.-specific C :::a:a:: probability G a:a::::a matrix T :a::::5: bits 2.8 * ** * * 2.5 * ** * * 2.2 * ** * * 1.9 * ** * * Relative 1.7 **** * * Entropy 1.4 ****** * (17.3 bits) 1.1 ****** * 0.8 ****** * 0.6 ******** 0.3 ******** 0.0 -------- Multilevel GTGCACAG consensus T sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GTGCACWG MEME-1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr3L:4393014-4393134 87 6.42e-06 TTTTCTTTCT GTGCACAG TGCCACCTCG chr3R:31712700-31712820 39 6.42e-06 GTGTGCCATC GTGCACAG CAAAACTAGT chr2R:10847409-10847529 13 6.42e-06 TACTGCATGG GTGCACAG TAAGAAAATA chr2R:21783562-21783682 12 6.42e-06 CGTGTTCAGC GTGCACTG AAAGAAAAAT chr3R:18492058-18492178 102 6.42e-06 CTTTCTCTCA GTGCACTG TTGTTGGTGG chr3L:14440735-14440855 59 6.42e-06 CTTAAATTCA GTGCACAG TGACTAAAGT chr3R:23392367-23392487 1 6.42e-06 . GTGCACTG AGAGAAACGC chr2L:4622064-4622184 1 6.42e-06 . GTGCACTG AAAACAATAT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GTGCACWG MEME-1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr3L:4393014-4393134 6.4e-06 86_[+1]_26 chr3R:31712700-31712820 6.4e-06 38_[+1]_74 chr2R:10847409-10847529 6.4e-06 12_[+1]_100 chr2R:21783562-21783682 6.4e-06 11_[+1]_101 chr3R:18492058-18492178 6.4e-06 101_[+1]_11 chr3L:14440735-14440855 6.4e-06 58_[+1]_54 chr3R:23392367-23392487 6.4e-06 [+1]_112 chr2L:4622064-4622184 6.4e-06 [+1]_112 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GTGCACWG MEME-1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF GTGCACWG width=8 seqs=8 chr3L:4393014-4393134 ( 87) GTGCACAG 1 chr3R:31712700-31712820 ( 39) GTGCACAG 1 chr2R:10847409-10847529 ( 13) GTGCACAG 1 chr2R:21783562-21783682 ( 12) GTGCACTG 1 chr3R:18492058-18492178 ( 102) GTGCACTG 1 chr3L:14440735-14440855 ( 59) GTGCACAG 1 chr3R:23392367-23392487 ( 1) GTGCACTG 1 chr2L:4622064-4622184 ( 1) GTGCACTG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GTGCACWG MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 28250 bayes= 10.9372 E= 2.7e+001 -965 -965 276 -965 -965 -965 -965 152 -965 -965 276 -965 -965 272 -965 -965 150 -965 -965 -965 -965 272 -965 -965 51 -965 -965 52 -965 -965 276 -965 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GTGCACWG MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 8 E= 2.7e+001 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 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.500000 0.000000 0.000000 0.500000 0.000000 0.000000 1.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GTGCACWG MEME-1 regular expression -------------------------------------------------------------------------------- GTGCAC[AT]G -------------------------------------------------------------------------------- Time 7.58 secs. ******************************************************************************** ******************************************************************************** MOTIF GGTGGCCC MEME-2 width = 8 sites = 4 llr = 51 E-value = 3.6e+003 ******************************************************************************** -------------------------------------------------------------------------------- Motif GGTGGCCC MEME-2 Description -------------------------------------------------------------------------------- Simplified A :::::::: pos.-specific C :::::a88 probability G aa3aa::3 matrix T ::8:::3: 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 GGTGGCCC consensus G TG sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGTGGCCC MEME-2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr3R:30312636-30312756 36 5.86e-07 AATGATTCAA GGTGGCCC CTTTTTGAAG chr3L:6396024-6396144 28 8.36e-07 ACTTCTTTAA GGGGGCCC AAAAACGAGA chr3L:17045808-17045928 70 1.41e-06 ACGAGCGATC GGTGGCCG TGGAAAACCA chr2L:20340761-20340881 59 2.99e-06 GACGAAAGAA GGTGGCTC TTTTTAGGAG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGTGGCCC MEME-2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr3R:30312636-30312756 5.9e-07 35_[+2]_77 chr3L:6396024-6396144 8.4e-07 27_[+2]_85 chr3L:17045808-17045928 1.4e-06 69_[+2]_43 chr2L:20340761-20340881 3e-06 58_[+2]_54 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGTGGCCC MEME-2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF GGTGGCCC width=8 seqs=4 chr3R:30312636-30312756 ( 36) GGTGGCCC 1 chr3L:6396024-6396144 ( 28) GGGGGCCC 1 chr3L:17045808-17045928 ( 70) GGTGGCCG 1 chr2L:20340761-20340881 ( 59) GGTGGCTC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGTGGCCC MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 28250 bayes= 13.5228 E= 3.6e+003 -865 -865 276 -865 -865 -865 276 -865 -865 -865 76 110 -865 -865 276 -865 -865 -865 276 -865 -865 271 -865 -865 -865 230 -865 -48 -865 230 76 -865 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGTGGCCC MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 4 E= 3.6e+003 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.250000 0.750000 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 0.750000 0.000000 0.250000 0.000000 0.750000 0.250000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGTGGCCC MEME-2 regular expression -------------------------------------------------------------------------------- GG[TG]GGC[CT][CG] -------------------------------------------------------------------------------- Time 13.94 secs. ******************************************************************************** ******************************************************************************** MOTIF GTGGCCAA MEME-3 width = 8 sites = 8 llr = 90 E-value = 4.6e+003 ******************************************************************************** -------------------------------------------------------------------------------- Motif GTGGCCAA MEME-3 Description -------------------------------------------------------------------------------- Simplified A ::::::a9 pos.-specific C 1:::aa:1 probability G 9:8a:::: matrix T :a3::::: bits 2.8 *** 2.5 *** 2.2 * *** 1.9 * *** Relative 1.7 ****** Entropy 1.4 ******* (16.2 bits) 1.1 ******** 0.8 ******** 0.6 ******** 0.3 ******** 0.0 -------- Multilevel GTGGCCAA consensus T sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GTGGCCAA MEME-3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr3R:19255371-19255491 24 3.23e-06 GTGAAAAAAT GTGGCCAA AAGCATAACT chr3R:14280486-14280606 97 3.23e-06 TATTGCATTT GTGGCCAA ATTAAAAAGT chrX:6745683-6745803 106 3.23e-06 ATTACATTAT GTGGCCAA GCATTTG chr3R:9480578-9480698 105 3.23e-06 GACACATGCA GTGGCCAA GTATCCCA chr3L:9209049-9209169 28 4.62e-06 CTTAGGAGCA GTGGCCAC ACAGAGAGAA chr2R:12736677-12736797 8 7.94e-06 AAATCGG CTGGCCAA TGAAGCTACA chr3L:2533150-2533270 98 1.55e-05 AATCGGGCAT GTTGCCAA CAATGATGTA chr3R:31314607-31314727 102 1.55e-05 GCAACTTAAT GTTGCCAA AATCTGCACC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GTGGCCAA MEME-3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr3R:19255371-19255491 3.2e-06 23_[+3]_89 chr3R:14280486-14280606 3.2e-06 96_[+3]_16 chrX:6745683-6745803 3.2e-06 105_[+3]_7 chr3R:9480578-9480698 3.2e-06 104_[+3]_8 chr3L:9209049-9209169 4.6e-06 27_[+3]_85 chr2R:12736677-12736797 7.9e-06 7_[+3]_105 chr3L:2533150-2533270 1.6e-05 97_[+3]_15 chr3R:31314607-31314727 1.6e-05 101_[+3]_11 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GTGGCCAA MEME-3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF GTGGCCAA width=8 seqs=8 chr3R:19255371-19255491 ( 24) GTGGCCAA 1 chr3R:14280486-14280606 ( 97) GTGGCCAA 1 chrX:6745683-6745803 ( 106) GTGGCCAA 1 chr3R:9480578-9480698 ( 105) GTGGCCAA 1 chr3L:9209049-9209169 ( 28) GTGGCCAC 1 chr2R:12736677-12736797 ( 8) CTGGCCAA 1 chr3L:2533150-2533270 ( 98) GTTGCCAA 1 chr3R:31314607-31314727 ( 102) GTTGCCAA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GTGGCCAA MEME-3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 28250 bayes= 11.7856 E= 4.6e+003 -965 -28 257 -965 -965 -965 -965 152 -965 -965 234 -48 -965 -965 276 -965 -965 272 -965 -965 -965 272 -965 -965 150 -965 -965 -965 131 -28 -965 -965 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GTGGCCAA MEME-3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 8 E= 4.6e+003 0.000000 0.125000 0.875000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.750000 0.250000 0.000000 0.000000 1.000000 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 0.875000 0.125000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GTGGCCAA MEME-3 regular expression -------------------------------------------------------------------------------- GT[GT]GCCAA -------------------------------------------------------------------------------- Time 20.29 secs. ******************************************************************************** ******************************************************************************** MOTIF GGCTCGTG MEME-4 width = 8 sites = 2 llr = 27 E-value = 1.0e+004 ******************************************************************************** -------------------------------------------------------------------------------- Motif GGCTCGTG MEME-4 Description -------------------------------------------------------------------------------- Simplified A :::::::: pos.-specific C ::a:a::: probability G aa:::a:a matrix T :::a::a: bits 2.8 *** ** * 2.5 *** ** * 2.2 *** ** * 1.9 *** ** * Relative 1.7 ******** Entropy 1.4 ******** (19.5 bits) 1.1 ******** 0.8 ******** 0.6 ******** 0.3 ******** 0.0 -------- Multilevel GGCTCGTG consensus sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGCTCGTG MEME-4 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr2L:20328753-20328873 31 1.34e-06 TGCCTCTTGT GGCTCGTG GTTTCGATGT chr3L:17045808-17045928 94 1.34e-06 ACCACTATAC GGCTCGTG TTCAGTCTCC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGCTCGTG MEME-4 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr2L:20328753-20328873 1.3e-06 30_[+4]_82 chr3L:17045808-17045928 1.3e-06 93_[+4]_19 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGCTCGTG MEME-4 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF GGCTCGTG width=8 seqs=2 chr2L:20328753-20328873 ( 31) GGCTCGTG 1 chr3L:17045808-17045928 ( 94) GGCTCGTG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGCTCGTG MEME-4 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 28250 bayes= 13.7859 E= 1.0e+004 -765 -765 275 -765 -765 -765 275 -765 -765 271 -765 -765 -765 -765 -765 152 -765 271 -765 -765 -765 -765 275 -765 -765 -765 -765 152 -765 -765 275 -765 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGCTCGTG MEME-4 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 2 E= 1.0e+004 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 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGCTCGTG MEME-4 regular expression -------------------------------------------------------------------------------- GGCTCGTG -------------------------------------------------------------------------------- Time 26.55 secs. ******************************************************************************** ******************************************************************************** MOTIF GGGTCGTC MEME-5 width = 8 sites = 2 llr = 27 E-value = 1.0e+004 ******************************************************************************** -------------------------------------------------------------------------------- Motif GGGTCGTC MEME-5 Description -------------------------------------------------------------------------------- Simplified A :::::::: pos.-specific C ::::a::a probability G aaa::a:: matrix T :::a::a: bits 2.8 *** ** * 2.5 *** ** * 2.2 *** ** * 1.9 *** ** * Relative 1.7 ******** Entropy 1.4 ******** (19.5 bits) 1.1 ******** 0.8 ******** 0.6 ******** 0.3 ******** 0.0 -------- Multilevel GGGTCGTC consensus sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGGTCGTC MEME-5 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr3R:24024270-24024390 18 1.34e-06 TAATGTGTTA GGGTCGTC TCCAATTTCT chr2R:10847409-10847529 33 1.34e-06 AGAAAATATT GGGTCGTC AATAGAGAAG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGGTCGTC MEME-5 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr3R:24024270-24024390 1.3e-06 17_[+5]_95 chr2R:10847409-10847529 1.3e-06 32_[+5]_80 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGGTCGTC MEME-5 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF GGGTCGTC width=8 seqs=2 chr3R:24024270-24024390 ( 18) GGGTCGTC 1 chr2R:10847409-10847529 ( 33) GGGTCGTC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGGTCGTC MEME-5 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 28250 bayes= 13.7859 E= 1.0e+004 -765 -765 275 -765 -765 -765 275 -765 -765 -765 275 -765 -765 -765 -765 152 -765 271 -765 -765 -765 -765 275 -765 -765 -765 -765 152 -765 271 -765 -765 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGGTCGTC MEME-5 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 2 E= 1.0e+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 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGGTCGTC MEME-5 regular expression -------------------------------------------------------------------------------- GGGTCGTC -------------------------------------------------------------------------------- Time 32.85 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr3R:18486302-18486422 6.64e-02 120 chr3R:18491264-18491384 5.37e-01 120 chrX:9654071-9654191 9.44e-01 120 chr3R:12315569-12315689 7.58e-03 120 chr3L:2162774-2162894 1.77e-01 120 chr3L:17045808-17045928 3.95e-07 69_[+2(1.41e-06)]_16_[+4(1.34e-06)]_\ 19 chr3L:21224452-21224572 9.41e-01 120 chr3R:10531949-10532069 4.03e-02 120 chr3L:18231576-18231696 9.16e-01 120 chr3R:29211876-29211996 4.12e-01 120 chr2L:734268-734388 3.06e-01 120 chr3R:19788904-19789024 6.29e-01 120 chr3L:4271577-4271697 5.57e-02 120 chr2L:4622064-4622184 2.38e-03 [+1(6.42e-06)]_112 chr2L:20328753-20328873 2.18e-04 30_[+4(1.34e-06)]_82 chr3L:14483126-14483246 2.46e-01 120 chr3L:5626613-5626733 1.11e-01 120 chr2R:18656795-18656915 4.87e-01 120 chr3R:23392367-23392487 8.36e-05 [+1(6.42e-06)]_81_[+4(5.23e-05)]_23 chr2R:7114733-7114853 4.46e-01 120 chr3R:26894035-26894155 5.86e-01 120 chr3L:1484881-1485001 6.15e-01 120 chr2L:14260001-14260121 4.24e-01 120 chr3R:21906985-21907105 5.46e-01 120 chr3L:17504723-17504843 5.30e-01 120 chr3L:3536539-3536659 9.47e-01 120 chr2R:14119316-14119436 5.84e-01 120 chr3L:18096882-18097002 3.22e-01 120 chrX:7637273-7637393 1.18e-01 120 chr2L:7513819-7513939 6.80e-01 120 chr3R:18488020-18488140 7.96e-01 120 chrX:13951549-13951669 5.51e-01 120 chr3R:10842538-10842658 1.72e-02 100_[+2(3.05e-05)]_12 chr3L:14440735-14440855 3.16e-02 58_[+1(6.42e-06)]_54 chr2R:7112254-7112374 1.00e+00 120 chr2L:4633157-4633277 4.89e-01 120 chr3R:22576218-22576338 9.07e-03 120 chr3L:4398048-4398168 5.61e-01 120 chr2L:4648941-4649061 5.22e-01 120 chr2R:12736677-12736797 4.50e-03 7_[+3(7.94e-06)]_105 chrX:4963114-4963234 6.69e-01 120 chr3L:3555238-3555358 9.57e-01 120 chrX:15639168-15639288 9.33e-01 120 chr3R:18492058-18492178 4.77e-02 101_[+1(6.42e-06)]_11 chr2R:22727164-22727284 9.63e-01 120 chr2R:13291883-13292003 9.64e-01 120 chrX:5924527-5924647 2.41e-01 120 chr2L:18752933-18753053 8.58e-01 120 chr3L:3791225-3791345 1.39e-02 120 chr2R:17496980-17497100 1.92e-01 120 chr2R:14083090-14083210 9.41e-01 120 chrX:10539243-10539363 9.71e-01 120 chr3R:31767652-31767772 2.20e-01 120 chr3L:9765337-9765457 7.10e-01 120 chr3L:12073247-12073367 2.14e-01 120 chr3R:8788028-8788148 1.00e+00 120 chr3R:31944356-31944476 9.04e-01 120 chr3L:4745278-4745398 6.79e-01 120 chr2R:15233472-15233592 3.52e-02 [+4(5.70e-05)]_112 chr3R:25451960-25452080 3.49e-01 120 chr3R:25644323-25644443 9.97e-01 120 chr2R:15599991-15600111 9.51e-01 120 chr2R:12739826-12739946 7.35e-02 120 chr3R:22400391-22400511 7.73e-01 120 chr3L:9745541-9745661 9.89e-01 120 chrX:4170623-4170743 9.99e-01 120 chr3L:18245930-18246050 6.35e-01 120 chr2L:4635521-4635641 7.11e-01 120 chr3L:10903547-10903667 9.99e-01 120 chr3L:22106841-22106961 9.50e-01 120 chr2L:684910-685030 8.59e-01 120 chr2L:1538253-1538373 8.90e-01 120 chr2L:18744015-18744135 9.80e-01 120 chr3R:26478169-26478289 3.20e-01 120 chr2R:21783562-21783682 8.49e-02 11_[+1(6.42e-06)]_101 chr3L:485494-485614 9.13e-01 120 chrX:838117-838237 3.31e-01 120 chr2R:7161980-7162100 8.69e-01 120 chr2R:21801104-21801224 4.04e-01 120 chr3R:18499458-18499578 6.90e-01 120 chr3L:6355162-6355282 2.57e-01 120 chrX:17686390-17686510 1.00e+00 120 chr2R:20143495-20143615 9.99e-01 120 chr2L:14413495-14413615 7.05e-01 120 chrX:724617-724737 2.73e-01 120 chrX:8747802-8747922 9.38e-01 120 chrX:5014793-5014913 7.00e-01 120 chr3L:16454657-16454777 5.28e-02 120 chr2R:12413294-12413414 2.77e-01 120 chr2L:18348779-18348899 9.61e-01 120 chr2R:12720724-12720844 9.92e-01 120 chr2R:20057880-20058000 2.66e-01 120 chr2R:19904084-19904204 9.57e-01 120 chr2L:7627601-7627721 9.29e-01 120 chr2R:10847409-10847529 1.16e-06 12_[+1(6.42e-06)]_12_[+5(1.34e-06)]_\ 80 chr3L:16454440-16454560 1.55e-01 120 chrX:18800298-18800418 4.54e-01 120 chr3R:19383455-19383575 8.84e-01 120 chr3R:17814317-17814437 9.42e-01 120 chr3R:22158372-22158492 3.03e-01 120 chr3R:4957936-4958056 6.78e-01 120 chr3R:11945606-11945726 9.91e-01 120 chr3L:15187917-15188037 1.00e+00 120 chrX:378443-378563 9.86e-01 120 chrX:15156410-15156530 7.26e-01 120 chr2L:661080-661200 1.56e-01 120 chr3L:5945719-5945839 1.00e+00 120 chr3L:21223425-21223545 9.99e-01 120 chr2R:6869570-6869690 2.58e-01 120 chr2R:8319977-8320097 1.58e-01 120 chr3R:18485390-18485510 2.84e-01 120 chr2L:18746853-18746973 9.60e-01 120 chr3R:30344676-30344796 7.98e-01 120 chr2R:8596670-8596790 3.38e-01 120 chr2R:16706829-16706949 8.23e-01 120 chr3R:31314607-31314727 4.04e-02 101_[+3(1.55e-05)]_11 chr2L:653936-654056 9.65e-01 120 chr2L:20840207-20840327 1.87e-01 120 chr3R:21979513-21979633 2.19e-01 120 chr3L:18245097-18245217 3.81e-01 120 chr3R:27181259-27181379 7.98e-01 120 chr3L:14616735-14616855 7.12e-02 120 chr3L:21237127-21237247 9.68e-01 120 chr3R:26479373-26479493 1.22e-01 120 chrX:8839530-8839650 5.71e-01 120 chr2R:20196898-20197018 5.14e-01 120 chrX:5013180-5013300 3.23e-01 120 chrX:8163581-8163701 9.96e-01 120 chrX:2796728-2796848 6.57e-01 120 chr3R:15113722-15113842 7.72e-01 120 chr3L:20988009-20988129 4.33e-01 120 chr3L:16019259-16019379 5.45e-01 120 chr2L:19936244-19936364 7.64e-01 120 chr3R:30872814-30872934 9.87e-01 120 chr3R:24024270-24024390 1.99e-03 17_[+5(1.34e-06)]_95 chr2L:15474512-15474632 9.99e-01 120 chrX:5038586-5038706 9.74e-01 120 chr2L:4797732-4797852 6.99e-01 120 chr3L:12072522-12072642 1.49e-01 120 chr3L:20983459-20983579 1.00e+00 120 chr2L:3645476-3645596 5.98e-01 120 chrX:11736554-11736674 4.22e-01 120 chr3L:17981240-17981360 9.66e-01 120 chr2L:18752169-18752289 3.95e-01 120 chr3R:9480578-9480698 2.06e-03 104_[+3(3.23e-06)]_8 chr3L:18076754-18076874 4.55e-02 120 chr2R:18663211-18663331 7.52e-01 120 chr2R:11315581-11315701 8.93e-01 120 chr3R:19070765-19070885 7.09e-01 120 chr3L:8319238-8319358 8.28e-01 120 chr3L:6308750-6308870 7.97e-01 120 chr2R:18569195-18569315 2.38e-01 120 chr3L:18248536-18248656 9.03e-01 120 chr2R:23198704-23198824 6.81e-01 120 chr3L:16751788-16751908 1.00e+00 120 chr2R:16710942-16711062 5.89e-01 120 chr3L:6396024-6396144 1.26e-03 27_[+2(8.36e-07)]_85 chr3L:7632978-7633098 9.88e-01 120 chrX:4959037-4959157 5.66e-01 120 chr3R:11616392-11616512 5.63e-01 120 chr2R:20055395-20055515 9.91e-01 120 chr2R:7622148-7622268 3.19e-01 120 chr3L:22192354-22192474 4.21e-01 120 chrX:18558756-18558876 5.96e-01 120 chr3L:12109367-12109487 7.09e-02 120 chr2R:18353624-18353744 8.15e-01 120 chr2R:6521299-6521419 9.89e-01 120 chr3L:6307414-6307534 9.80e-01 120 chr2R:17243852-17243972 8.30e-01 120 chr3R:7025388-7025508 1.85e-01 120 chr2L:19317945-19318065 4.32e-01 120 chr2R:20568436-20568556 1.08e-01 120 chr2L:20328077-20328197 8.75e-01 120 chrX:3739278-3739398 8.32e-01 120 chrX:17112145-17112265 9.07e-01 120 chrX:23071347-23071467 1.33e-01 120 chr2L:20335071-20335191 1.92e-01 120 chr2R:8596870-8596990 9.62e-01 120 chr3L:14462481-14462601 1.24e-02 108_[+1(3.30e-05)]_4 chr3R:13797456-13797576 9.99e-01 120 chr3R:31712700-31712820 9.68e-03 38_[+1(6.42e-06)]_74 chr3R:13875545-13875665 3.28e-01 120 chr3L:767066-767186 8.93e-01 120 chr3L:2486626-2486746 4.97e-02 120 chr3L:4393014-4393134 7.08e-03 86_[+1(6.42e-06)]_26 chr2L:20340761-20340881 1.44e-03 58_[+2(2.99e-06)]_54 chr3L:9209252-9209372 4.39e-01 120 chr3L:4346472-4346592 5.71e-01 120 chr2R:23306111-23306231 2.11e-01 120 chr3R:30567365-30567485 2.28e-01 120 chr3L:741832-741952 9.96e-01 120 chr3R:19075275-19075395 9.49e-01 120 chr2L:5495097-5495217 9.49e-01 120 chr3R:14720227-14720347 7.15e-02 120 chrX:4999142-4999262 3.42e-01 120 chr3L:9765537-9765657 2.75e-02 39_[+5(5.23e-05)]_73 chr3L:4336683-4336803 9.88e-01 120 chr2R:8645858-8645978 8.74e-01 120 chrX:14922538-14922658 1.15e-01 120 chr3R:27685594-27685714 1.00e+00 120 chr2R:21531619-21531739 5.70e-01 120 chr3R:29072965-29073085 9.91e-01 120 chrX:6745683-6745803 8.04e-03 105_[+3(3.23e-06)]_7 chr2L:21246812-21246932 8.73e-01 120 chr3L:16464079-16464199 6.41e-02 120 chr3L:10396693-10396813 5.97e-01 120 chr2L:20370278-20370398 9.92e-01 120 chr3L:14422303-14422423 8.97e-01 120 chr2R:17077070-17077190 5.12e-01 120 chr3R:30312636-30312756 3.11e-04 35_[+2(5.86e-07)]_77 chrX:9738618-9738738 8.82e-01 120 chr2R:17811086-17811206 1.96e-01 120 chr3R:14280486-14280606 1.51e-03 96_[+3(3.23e-06)]_16 chr2R:12534446-12534566 8.38e-01 120 chr3L:590009-590129 1.29e-01 120 chr3L:20914560-20914680 9.82e-01 120 chrX:11544702-11544822 1.00e+00 120 chr2L:19574574-19574694 2.74e-01 120 chr2R:21377333-21377453 9.79e-01 120 chr2L:16281790-16281910 1.00e+00 120 chr3R:26019349-26019469 6.61e-01 120 chr2R:14081668-14081788 3.96e-01 120 chr3R:15567109-15567229 3.76e-01 120 chr2R:21550607-21550727 8.51e-01 120 chr3L:9209049-9209169 1.27e-03 27_[+3(4.62e-06)]_85 chr3L:6266238-6266358 2.92e-02 120 chr3R:22594398-22594518 3.61e-01 120 chrX:293439-293559 9.06e-01 120 chr2L:20721590-20721710 9.30e-01 120 chr3R:22150084-22150204 9.86e-01 120 chrX:15123567-15123687 9.77e-01 120 chrX:17914639-17914759 9.72e-01 120 chr3L:18248852-18248972 3.92e-02 120 chr2R:5781960-5782080 2.79e-03 36_[+4(5.23e-05)]_76 chr3R:4687363-4687483 9.73e-01 120 chr2R:14317129-14317249 9.92e-01 120 chr2R:22142236-22142356 1.96e-01 120 chr3R:19074399-19074519 3.52e-01 120 chr3L:2533150-2533270 7.95e-02 97_[+3(1.55e-05)]_15 chr3R:21895992-21896112 9.68e-01 120 chr2R:16212935-16213055 9.42e-01 120 chr3R:19255371-19255491 9.05e-04 23_[+3(3.23e-06)]_89 chr3R:6214371-6214491 2.40e-01 120 chrX:19173107-19173227 7.63e-01 120 chr3L:14145782-14145902 6.69e-01 120 chr3L:11444279-11444399 1.00e+00 120 chr2L:1388008-1388128 6.48e-01 120 chr2R:8646570-8646690 5.76e-01 120 chr2L:4065326-4065446 9.69e-01 120 chr2L:7971523-7971643 1.00e+00 120 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (5) found. ******************************************************************************** CPU: c28n07.farnam.hpc.yale.internal ********************************************************************************