******************************************************************************** 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/CG7839.fasta CONTROL SEQUENCES= --none-- ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ chr3R:25754938-25755058 1.0000 120 chr3R:13803990-13804110 1.0000 120 chrX:3109047-3109167 1.0000 120 chr3L:1609769-1609889 1.0000 120 chr3L:3786897-3787017 1.0000 120 chr3L:6807644-6807764 1.0000 120 chrX:10397714-10397834 1.0000 120 chr2R:10160417-10160537 1.0000 120 chr2L:16869113-16869233 1.0000 120 chr3R:21612990-21613110 1.0000 120 chr2L:17558213-17558333 1.0000 120 chr3L:19338405-19338525 1.0000 120 chr3L:11285257-11285377 1.0000 120 chr2R:8759575-8759695 1.0000 120 chr2R:7879082-7879202 1.0000 120 chr3R:8810995-8811115 1.0000 120 chr3R:21887665-21887785 1.0000 120 chrX:17762419-17762539 1.0000 120 chr2R:15155039-15155159 1.0000 120 chr2R:18374625-18374745 1.0000 120 chr3R:24026254-24026374 1.0000 120 chr3R:26409919-26410039 1.0000 120 chr3L:16840637-16840757 1.0000 120 chrX:8206026-8206146 1.0000 120 chr3R:26242596-26242716 1.0000 120 chr3R:22121364-22121484 1.0000 120 chr3L:2581990-2582110 1.0000 120 chrX:13208227-13208347 1.0000 120 chr2R:7896320-7896440 1.0000 120 chrX:12937947-12938067 1.0000 120 chr3L:10786062-10786182 1.0000 120 chr3L:11272842-11272962 1.0000 120 chr3L:3970526-3970646 1.0000 120 chr3R:6414893-6415013 1.0000 120 chr2L:2872704-2872824 1.0000 120 chrX:14593251-14593371 1.0000 120 chrX:10741103-10741223 1.0000 120 chrX:14840653-14840773 1.0000 120 chr3L:16149967-16150087 1.0000 120 chr2R:17205990-17206110 1.0000 120 chr3L:10893544-10893664 1.0000 120 chr3L:10756188-10756308 1.0000 120 chrX:3455553-3455673 1.0000 120 chr3R:13446638-13446758 1.0000 120 chr2R:6219942-6220062 1.0000 120 chr3R:18438883-18439003 1.0000 120 chrX:19106986-19107106 1.0000 120 chr3L:13356185-13356305 1.0000 120 chr2R:22384454-22384574 1.0000 120 chr3L:18402690-18402810 1.0000 120 chr2L:8746405-8746525 1.0000 120 chrX:9004483-9004603 1.0000 120 chrX:3096436-3096556 1.0000 120 chr2R:13996720-13996840 1.0000 120 chr3R:29626011-29626131 1.0000 120 chrX:5989497-5989617 1.0000 120 chr2L:7150939-7151059 1.0000 120 chr3L:12223088-12223208 1.0000 120 chrX:14727723-14727843 1.0000 120 chr3L:14205091-14205211 1.0000 120 chr3R:10688945-10689065 1.0000 120 chr2L:18906739-18906859 1.0000 120 chr3R:22878550-22878670 1.0000 120 chr3L:110083-110203 1.0000 120 chrX:17696804-17696924 1.0000 120 chr2L:14537582-14537702 1.0000 120 chr3L:19216519-19216639 1.0000 120 chr3R:16476579-16476699 1.0000 120 chr2R:14305245-14305365 1.0000 120 chr2R:18273451-18273571 1.0000 120 chrX:9350411-9350531 1.0000 120 chr2R:11044564-11044684 1.0000 120 chr2L:13905441-13905561 1.0000 120 chr3L:7634877-7634997 1.0000 120 chr2L:18658219-18658339 1.0000 120 chr2R:13261849-13261969 1.0000 120 chr3L:19087998-19088118 1.0000 120 chr2R:24139211-24139331 1.0000 120 chr2L:13572210-13572330 1.0000 120 chr3L:15923486-15923606 1.0000 120 chrX:19964329-19964449 1.0000 120 chr2L:9564658-9564778 1.0000 120 chrX:16580083-16580203 1.0000 120 chr3R:9494361-9494481 1.0000 120 chrX:3019708-3019828 1.0000 120 chr2L:19252543-19252663 1.0000 120 chr3L:15275607-15275727 1.0000 120 chr2L:17588799-17588919 1.0000 120 chrX:7691523-7691643 1.0000 120 chr2L:7541486-7541606 1.0000 120 chr2L:14024820-14024940 1.0000 120 chr2R:9388673-9388793 1.0000 120 chrX:11379272-11379392 1.0000 120 chrX:10184795-10184915 1.0000 120 chr3L:15977739-15977859 1.0000 120 chr3R:10636152-10636272 1.0000 120 chrX:7703115-7703235 1.0000 120 chr3L:16146662-16146782 1.0000 120 chr3R:20555134-20555254 1.0000 120 chr2L:1619317-1619437 1.0000 120 chr2R:16581768-16581888 1.0000 120 chr3R:28959231-28959351 1.0000 120 chr2L:14252535-14252655 1.0000 120 chrX:17330408-17330528 1.0000 120 chr3L:19073957-19074077 1.0000 120 chrX:19146448-19146568 1.0000 120 chr2R:8734612-8734732 1.0000 120 chrX:6090961-6091081 1.0000 120 chr2R:17469469-17469589 1.0000 120 chr3L:2845325-2845445 1.0000 120 chr3L:8629048-8629168 1.0000 120 chr3R:11663607-11663727 1.0000 120 chr2R:12727660-12727780 1.0000 120 chr2L:14441029-14441149 1.0000 120 chrX:8493614-8493734 1.0000 120 chr2R:11178549-11178669 1.0000 120 chr3R:28327361-28327481 1.0000 120 chr2L:14376932-14377052 1.0000 120 chrX:10573644-10573764 1.0000 120 chr3R:21188174-21188294 1.0000 120 chrX:947621-947741 1.0000 120 chr2R:18435168-18435288 1.0000 120 chr3L:16054246-16054366 1.0000 120 chr3R:18670554-18670674 1.0000 120 chr3R:25184183-25184303 1.0000 120 chr3R:26014391-26014511 1.0000 120 chr2R:23578560-23578680 1.0000 120 chr3R:29581627-29581747 1.0000 120 chr2L:11331804-11331924 1.0000 120 chr2L:7492028-7492148 1.0000 120 chr3L:2651902-2652022 1.0000 120 chrX:17293543-17293663 1.0000 120 chrX:9119424-9119544 1.0000 120 chr2L:12542120-12542240 1.0000 120 chrX:14743902-14744022 1.0000 120 chr3L:5926088-5926208 1.0000 120 chr2L:9235652-9235772 1.0000 120 chr3R:19627920-19628040 1.0000 120 chr3R:23969549-23969669 1.0000 120 chr3L:15034475-15034595 1.0000 120 chrX:3399389-3399509 1.0000 120 chr3L:12271462-12271582 1.0000 120 chr2R:12547649-12547769 1.0000 120 chr3L:7592231-7592351 1.0000 120 chr3R:9237935-9238055 1.0000 120 chrX:16834358-16834478 1.0000 120 chr3R:28676998-28677118 1.0000 120 chr3L:18030015-18030135 1.0000 120 chr3L:18272435-18272555 1.0000 120 chrX:8677559-8677679 1.0000 120 chr2R:12035181-12035301 1.0000 120 chr2L:3880230-3880350 1.0000 120 chrX:14679305-14679425 1.0000 120 chrX:7703369-7703489 1.0000 120 chr2L:10760735-10760855 1.0000 120 chr3L:3437279-3437399 1.0000 120 chr3L:10767326-10767446 1.0000 120 chr2L:19930253-19930373 1.0000 120 chrX:8542115-8542235 1.0000 120 chr2R:11809470-11809590 1.0000 120 chr2L:7871930-7872050 1.0000 120 chrX:16930474-16930594 1.0000 120 chr2R:10123662-10123782 1.0000 120 chr3R:16223765-16223885 1.0000 120 chr3R:10520688-10520808 1.0000 120 chrX:16103563-16103683 1.0000 120 chrX:1270775-1270895 1.0000 120 chr3L:16202724-16202844 1.0000 120 chrX:8444947-8445067 1.0000 120 chrX:13764540-13764660 1.0000 120 chr3L:797030-797150 1.0000 120 chrX:9120973-9121093 1.0000 120 chr3L:18782219-18782339 1.0000 120 chr3R:21993044-21993164 1.0000 120 chr3R:26117830-26117950 1.0000 120 chrX:18899960-18900080 1.0000 120 chrX:10825474-10825594 1.0000 120 chr2R:10854275-10854395 1.0000 120 chr2L:21149217-21149337 1.0000 120 chrX:12925973-12926093 1.0000 120 chrX:9899803-9899923 1.0000 120 chr2L:15908601-15908721 1.0000 120 chr3L:5554505-5554625 1.0000 120 chr2L:8894386-8894506 1.0000 120 chrX:16944149-16944269 1.0000 120 chr2R:11601954-11602074 1.0000 120 chr3R:11852077-11852197 1.0000 120 chr3R:25168354-25168474 1.0000 120 chr2R:16097052-16097172 1.0000 120 chr3L:22471687-22471807 1.0000 120 chrX:2396635-2396755 1.0000 120 chr3L:15691331-15691451 1.0000 120 chr2L:7395908-7396028 1.0000 120 chr3L:14363260-14363380 1.0000 120 chr2L:1207597-1207717 1.0000 120 chr3R:18393588-18393708 1.0000 120 chr2L:19517415-19517535 1.0000 120 chr2R:7054309-7054429 1.0000 120 chrX:4262809-4262929 1.0000 120 chrX:16854865-16854985 1.0000 120 chrX:2011727-2011847 1.0000 120 chr2R:7254319-7254439 1.0000 120 chr2L:9493408-9493528 1.0000 120 chr2L:15442301-15442421 1.0000 120 chr2L:8982713-8982833 1.0000 120 chr2R:12772801-12772921 1.0000 120 chr2L:19140991-19141111 1.0000 120 chr3L:15592662-15592782 1.0000 120 chr2R:15034876-15034996 1.0000 120 chr3R:26012956-26013076 1.0000 120 chr2R:19860399-19860519 1.0000 120 chr3R:8955033-8955153 1.0000 120 chr2L:21096500-21096620 1.0000 120 chr3R:12720113-12720233 1.0000 120 chr3R:14875713-14875833 1.0000 120 chr3L:8951128-8951248 1.0000 120 chr3L:13923456-13923576 1.0000 120 chrX:10628972-10629092 1.0000 120 chrX:10387790-10387910 1.0000 120 chr2R:10077914-10078034 1.0000 120 chrX:14169195-14169315 1.0000 120 chr3L:9691276-9691396 1.0000 120 chr3L:554722-554842 1.0000 120 chrX:3690733-3690853 1.0000 120 chr3R:8867848-8867968 1.0000 120 chr2R:13008285-13008405 1.0000 120 chrX:6375802-6375922 1.0000 120 chr3R:26444254-26444374 1.0000 120 chrX:16650541-16650661 1.0000 120 chrX:15297183-15297303 1.0000 120 chr3R:21493684-21493804 1.0000 120 chr3R:17535310-17535430 1.0000 120 chr3L:6157739-6157859 1.0000 120 chr3L:13905658-13905778 1.0000 120 chr2L:20759934-20760054 1.0000 120 chr3R:11661872-11661992 1.0000 120 chr3L:10745678-10745798 1.0000 120 chr2L:2905204-2905324 1.0000 120 chr3R:18311392-18311512 1.0000 120 chr2L:7270411-7270531 1.0000 120 chr3R:26888428-26888548 1.0000 120 chr2R:11435202-11435322 1.0000 120 chr3R:24010986-24011106 1.0000 120 chrX:21322736-21322856 1.0000 120 chr3R:25445643-25445763 1.0000 120 chr2L:7957102-7957222 1.0000 120 chrX:15384097-15384217 1.0000 120 chr2R:15240263-15240383 1.0000 120 chr3L:7861180-7861300 1.0000 120 chrX:13274596-13274716 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_CG7839/ -dna -nmotifs 5 -w 8 -maxsize 250000 -nostatus ../result/final_prediction/fly/fasta/RankLinear8.0_60/CG7839.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 0.372 C 0.129 G 0.13 T 0.369 Background letter frequencies (from file dataset with add-one prior applied): A 0.372 C 0.129 G 0.13 T 0.369 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF KCCCCGCG MEME-1 width = 8 sites = 2 llr = 30 E-value = 2.8e+003 ******************************************************************************** -------------------------------------------------------------------------------- Motif KCCCCGCG MEME-1 Description -------------------------------------------------------------------------------- Simplified A :::::::: pos.-specific C :aaaa:a: probability G 5::::a:a matrix T 5::::::: bits 3.0 ******* 2.7 ******* 2.4 ******* 2.1 ******* Relative 1.8 ******* Entropy 1.5 ******* (21.8 bits) 1.2 ******** 0.9 ******** 0.6 ******** 0.3 ******** 0.0 -------- Multilevel GCCCCGCG consensus T sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif KCCCCGCG MEME-1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr3L:1609769-1609889 98 7.85e-08 TTATTCGACA GCCCCGCG ACAACAACAG chr2R:22384454-22384574 76 3.01e-07 TTTAGATAAT TCCCCGCG TGGCTTTCAT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif KCCCCGCG MEME-1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr3L:1609769-1609889 7.8e-08 97_[+1]_15 chr2R:22384454-22384574 3e-07 75_[+1]_37 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif KCCCCGCG MEME-1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF KCCCCGCG width=8 seqs=2 chr3L:1609769-1609889 ( 98) GCCCCGCG 1 chr2R:22384454-22384574 ( 76) TCCCCGCG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif KCCCCGCG MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 28250 bayes= 13.7859 E= 2.8e+003 -765 -765 194 44 -765 295 -765 -765 -765 295 -765 -765 -765 295 -765 -765 -765 295 -765 -765 -765 -765 293 -765 -765 295 -765 -765 -765 -765 293 -765 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif KCCCCGCG MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 2 E= 2.8e+003 0.000000 0.000000 0.500000 0.500000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif KCCCCGCG MEME-1 regular expression -------------------------------------------------------------------------------- [GT]CCCCGCG -------------------------------------------------------------------------------- Time 7.66 secs. ******************************************************************************** ******************************************************************************** MOTIF GACCTGCG MEME-2 width = 8 sites = 2 llr = 28 E-value = 1.5e+004 ******************************************************************************** -------------------------------------------------------------------------------- Motif GACCTGCG MEME-2 Description -------------------------------------------------------------------------------- Simplified A :a:::::: pos.-specific C ::aa::a: probability G a::::a:a matrix T ::::a::: bits 3.0 * ** *** 2.7 * ** *** 2.4 * ** *** 2.1 * ** *** Relative 1.8 * ** *** Entropy 1.5 ******** (20.5 bits) 1.2 ******** 0.9 ******** 0.6 ******** 0.3 ******** 0.0 -------- Multilevel GACCTGCG consensus sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GACCTGCG MEME-2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr2L:21149217-21149337 79 6.47e-07 cagtgcttgg gacctgcg agtttaagat chrX:3019708-3019828 84 6.47e-07 ATATCAATTT GACCTGCG TACTTCCTGT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GACCTGCG MEME-2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr2L:21149217-21149337 6.5e-07 78_[+2]_34 chrX:3019708-3019828 6.5e-07 83_[+2]_29 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GACCTGCG MEME-2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF GACCTGCG width=8 seqs=2 chr2L:21149217-21149337 ( 79) GACCTGCG 1 chrX:3019708-3019828 ( 84) GACCTGCG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GACCTGCG MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 28250 bayes= 13.7859 E= 1.5e+004 -765 -765 293 -765 142 -765 -765 -765 -765 295 -765 -765 -765 295 -765 -765 -765 -765 -765 143 -765 -765 293 -765 -765 295 -765 -765 -765 -765 293 -765 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GACCTGCG MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 2 E= 1.5e+004 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 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 0.000000 1.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GACCTGCG MEME-2 regular expression -------------------------------------------------------------------------------- GACCTGCG -------------------------------------------------------------------------------- Time 14.05 secs. ******************************************************************************** ******************************************************************************** MOTIF CCCTGSAS MEME-3 width = 8 sites = 2 llr = 26 E-value = 4.2e+004 ******************************************************************************** -------------------------------------------------------------------------------- Motif CCCTGSAS MEME-3 Description -------------------------------------------------------------------------------- Simplified A ::::::a: pos.-specific C aaa::5:5 probability G ::::a5:5 matrix T :::a:::: bits 3.0 *** * 2.7 *** * 2.4 *** * 2.1 *** ** * Relative 1.8 *** ** * Entropy 1.5 ******** (18.6 bits) 1.2 ******** 0.9 ******** 0.6 ******** 0.3 ******** 0.0 -------- Multilevel CCCTGCAC consensus G G sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCCTGSAS MEME-3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr2L:2872704-2872824 104 6.37e-07 CCCACTGATA CCCTGCAC TGAGGTATT chr2R:11809470-11809590 10 2.57e-06 TATTTGCTA CCCTGGAG TTATCACGCT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCCTGSAS MEME-3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr2L:2872704-2872824 6.4e-07 103_[+3]_9 chr2R:11809470-11809590 2.6e-06 9_[+3]_103 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCCTGSAS MEME-3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF CCCTGSAS width=8 seqs=2 chr2L:2872704-2872824 ( 104) CCCTGCAC 1 chr2R:11809470-11809590 ( 10) CCCTGGAG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCCTGSAS MEME-3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 28250 bayes= 13.7859 E= 4.2e+004 -765 295 -765 -765 -765 295 -765 -765 -765 295 -765 -765 -765 -765 -765 143 -765 -765 293 -765 -765 195 194 -765 142 -765 -765 -765 -765 195 194 -765 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCCTGSAS MEME-3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 2 E= 4.2e+004 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.500000 0.500000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.500000 0.500000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCCTGSAS MEME-3 regular expression -------------------------------------------------------------------------------- CCCTG[CG]A[CG] -------------------------------------------------------------------------------- Time 20.38 secs. ******************************************************************************** ******************************************************************************** MOTIF CACWGCGG MEME-4 width = 8 sites = 2 llr = 27 E-value = 4.3e+004 ******************************************************************************** -------------------------------------------------------------------------------- Motif CACWGCGG MEME-4 Description -------------------------------------------------------------------------------- Simplified A :a:5:::: pos.-specific C a:a::a:: probability G ::::a:aa matrix T :::5:::: bits 3.0 * * **** 2.7 * * **** 2.4 * * **** 2.1 * * **** Relative 1.8 * * **** Entropy 1.5 *** **** (19.5 bits) 1.2 *** **** 0.9 *** **** 0.6 *** **** 0.3 ******** 0.0 -------- Multilevel CACAGCGG consensus T sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CACWGCGG MEME-4 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chrX:10387790-10387910 24 1.30e-06 GACGGAAGAA CACAGCGG AAAAGGAAAA chrX:16580083-16580203 49 1.30e-06 AATCCGAATT CACTGCGG AAGATGCCCT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CACWGCGG MEME-4 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrX:10387790-10387910 1.3e-06 23_[+4]_89 chrX:16580083-16580203 1.3e-06 48_[+4]_64 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CACWGCGG MEME-4 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF CACWGCGG width=8 seqs=2 chrX:10387790-10387910 ( 24) CACAGCGG 1 chrX:16580083-16580203 ( 49) CACTGCGG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CACWGCGG MEME-4 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 28250 bayes= 12.9378 E= 4.3e+004 -765 295 -765 -765 142 -765 -765 -765 -765 295 -765 -765 43 -765 -765 44 -765 -765 293 -765 -765 295 -765 -765 -765 -765 293 -765 -765 -765 293 -765 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CACWGCGG MEME-4 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 2 E= 4.3e+004 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 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CACWGCGG MEME-4 regular expression -------------------------------------------------------------------------------- CAC[AT]GCGG -------------------------------------------------------------------------------- Time 26.68 secs. ******************************************************************************** ******************************************************************************** MOTIF GTGCCTAC MEME-5 width = 8 sites = 2 llr = 26 E-value = 6.3e+004 ******************************************************************************** -------------------------------------------------------------------------------- Motif GTGCCTAC MEME-5 Description -------------------------------------------------------------------------------- Simplified A ::::::a: pos.-specific C :::aa::a probability G a:a::::: matrix T :a:::a:: bits 3.0 * *** * 2.7 * *** * 2.4 * *** * 2.1 * *** * Relative 1.8 * *** * Entropy 1.5 ******** (19.0 bits) 1.2 ******** 0.9 ******** 0.6 ******** 0.3 ******** 0.0 -------- Multilevel GTGCCTAC consensus sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GTGCCTAC MEME-5 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr2R:11435202-11435322 86 1.84e-06 CATACAAAGT GTGCCTAC GTTGTTTTCG chrX:3019708-3019828 9 1.84e-06 AAGGTGCA GTGCCTAC AAACGGAGGG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GTGCCTAC MEME-5 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr2R:11435202-11435322 1.8e-06 85_[+5]_27 chrX:3019708-3019828 1.8e-06 8_[+5]_104 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GTGCCTAC MEME-5 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF GTGCCTAC width=8 seqs=2 chr2R:11435202-11435322 ( 86) GTGCCTAC 1 chrX:3019708-3019828 ( 9) GTGCCTAC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GTGCCTAC MEME-5 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 28250 bayes= 12.9378 E= 6.3e+004 -765 -765 293 -765 -765 -765 -765 143 -765 -765 293 -765 -765 295 -765 -765 -765 295 -765 -765 -765 -765 -765 143 142 -765 -765 -765 -765 295 -765 -765 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GTGCCTAC MEME-5 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 2 E= 6.3e+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 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GTGCCTAC MEME-5 regular expression -------------------------------------------------------------------------------- GTGCCTAC -------------------------------------------------------------------------------- Time 33.01 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr3R:25754938-25755058 9.80e-01 120 chr3R:13803990-13804110 9.98e-01 120 chrX:3109047-3109167 9.97e-01 120 chr3L:1609769-1609889 4.39e-07 97_[+1(7.85e-08)]_15 chr3L:3786897-3787017 3.24e-01 120 chr3L:6807644-6807764 5.92e-01 120 chrX:10397714-10397834 1.68e-02 120 chr2R:10160417-10160537 6.73e-01 120 chr2L:16869113-16869233 1.00e+00 120 chr3R:21612990-21613110 2.88e-04 3_[+3(9.10e-06)]_74_[+5(7.30e-05)]_\ 27 chr2L:17558213-17558333 9.80e-01 120 chr3L:19338405-19338525 9.52e-01 120 chr3L:11285257-11285377 9.69e-01 120 chr2R:8759575-8759695 8.19e-01 120 chr2R:7879082-7879202 6.54e-01 120 chr3R:8810995-8811115 1.83e-02 120 chr3R:21887665-21887785 9.17e-01 120 chrX:17762419-17762539 1.95e-01 120 chr2R:15155039-15155159 5.26e-01 120 chr2R:18374625-18374745 9.65e-01 120 chr3R:24026254-24026374 4.07e-01 120 chr3R:26409919-26410039 5.39e-01 120 chr3L:16840637-16840757 8.92e-01 120 chrX:8206026-8206146 9.66e-01 120 chr3R:26242596-26242716 6.56e-01 120 chr3R:22121364-22121484 6.77e-01 120 chr3L:2581990-2582110 8.96e-01 120 chrX:13208227-13208347 9.84e-01 120 chr2R:7896320-7896440 8.31e-01 120 chrX:12937947-12938067 1.00e+00 120 chr3L:10786062-10786182 6.86e-01 120 chr3L:11272842-11272962 5.48e-01 120 chr3L:3970526-3970646 3.00e-02 120 chr3R:6414893-6415013 9.98e-01 120 chr2L:2872704-2872824 5.89e-07 103_[+3(6.37e-07)]_9 chrX:14593251-14593371 7.36e-03 120 chrX:10741103-10741223 9.95e-01 120 chrX:14840653-14840773 9.56e-01 120 chr3L:16149967-16150087 6.55e-03 120 chr2R:17205990-17206110 3.17e-01 120 chr3L:10893544-10893664 1.00e+00 120 chr3L:10756188-10756308 7.78e-01 120 chrX:3455553-3455673 8.11e-01 120 chr3R:13446638-13446758 8.22e-01 120 chr2R:6219942-6220062 5.45e-01 120 chr3R:18438883-18439003 9.33e-01 120 chrX:19106986-19107106 3.44e-01 120 chr3L:13356185-13356305 1.35e-01 120 chr2R:22384454-22384574 1.09e-04 75_[+1(3.01e-07)]_37 chr3L:18402690-18402810 9.95e-01 120 chr2L:8746405-8746525 9.82e-01 120 chrX:9004483-9004603 5.33e-01 120 chrX:3096436-3096556 5.81e-01 120 chr2R:13996720-13996840 9.89e-01 120 chr3R:29626011-29626131 8.39e-01 120 chrX:5989497-5989617 5.55e-01 120 chr2L:7150939-7151059 3.47e-01 120 chr3L:12223088-12223208 6.97e-01 120 chrX:14727723-14727843 5.46e-02 120 chr3L:14205091-14205211 8.51e-01 120 chr3R:10688945-10689065 9.81e-01 120 chr2L:18906739-18906859 9.92e-01 120 chr3R:22878550-22878670 4.55e-01 120 chr3L:110083-110203 3.65e-01 120 chrX:17696804-17696924 8.10e-01 120 chr2L:14537582-14537702 2.41e-01 120 chr3L:19216519-19216639 8.36e-01 120 chr3R:16476579-16476699 4.42e-02 120 chr2R:14305245-14305365 9.08e-01 120 chr2R:18273451-18273571 7.03e-01 120 chrX:9350411-9350531 9.95e-01 120 chr2R:11044564-11044684 2.13e-01 120 chr2L:13905441-13905561 2.98e-01 120 chr3L:7634877-7634997 4.54e-01 120 chr2L:18658219-18658339 9.99e-01 120 chr2R:13261849-13261969 5.88e-01 120 chr3L:19087998-19088118 3.53e-01 120 chr2R:24139211-24139331 5.33e-02 79_[+3(9.53e-05)]_33 chr2L:13572210-13572330 1.00e+00 120 chr3L:15923486-15923606 7.70e-01 120 chrX:19964329-19964449 4.70e-01 120 chr2L:9564658-9564778 7.93e-01 120 chrX:16580083-16580203 1.59e-05 48_[+4(1.30e-06)]_64 chr3R:9494361-9494481 8.39e-01 120 chrX:3019708-3019828 4.45e-08 8_[+5(1.84e-06)]_67_[+2(6.47e-07)]_\ 29 chr2L:19252543-19252663 4.95e-01 120 chr3L:15275607-15275727 9.95e-01 120 chr2L:17588799-17588919 9.88e-01 120 chrX:7691523-7691643 1.30e-02 120 chr2L:7541486-7541606 9.99e-01 120 chr2L:14024820-14024940 3.03e-01 120 chr2R:9388673-9388793 8.18e-01 120 chrX:11379272-11379392 1.68e-01 120 chrX:10184795-10184915 6.49e-01 120 chr3L:15977739-15977859 7.84e-01 120 chr3R:10636152-10636272 1.79e-02 12_[+3(4.32e-05)]_100 chrX:7703115-7703235 9.92e-01 120 chr3L:16146662-16146782 9.88e-01 120 chr3R:20555134-20555254 9.81e-01 120 chr2L:1619317-1619437 1.36e-01 120 chr2R:16581768-16581888 3.01e-01 120 chr3R:28959231-28959351 9.96e-01 120 chr2L:14252535-14252655 3.90e-01 120 chrX:17330408-17330528 9.54e-01 120 chr3L:19073957-19074077 1.00e+00 120 chrX:19146448-19146568 5.74e-01 120 chr2R:8734612-8734732 1.02e-03 43_[+3(4.74e-06)]_69 chrX:6090961-6091081 7.59e-04 109_[+5(1.84e-06)]_3 chr2R:17469469-17469589 2.08e-02 79_[+5(7.30e-05)]_33 chr3L:2845325-2845445 7.25e-01 120 chr3L:8629048-8629168 7.15e-01 120 chr3R:11663607-11663727 8.81e-01 120 chr2R:12727660-12727780 9.19e-01 120 chr2L:14441029-14441149 5.29e-01 120 chrX:8493614-8493734 7.20e-02 21_[+2(2.90e-05)]_91 chr2R:11178549-11178669 3.44e-01 120 chr3R:28327361-28327481 1.52e-01 120 chr2L:14376932-14377052 2.51e-01 120 chrX:10573644-10573764 9.74e-01 120 chr3R:21188174-21188294 8.37e-01 120 chrX:947621-947741 4.30e-01 120 chr2R:18435168-18435288 8.92e-01 120 chr3L:16054246-16054366 8.69e-01 120 chr3R:18670554-18670674 9.86e-01 120 chr3R:25184183-25184303 9.99e-01 120 chr3R:26014391-26014511 2.13e-01 120 chr2R:23578560-23578680 5.36e-01 120 chr3R:29581627-29581747 6.65e-01 120 chr2L:11331804-11331924 5.72e-01 120 chr2L:7492028-7492148 7.60e-01 120 chr3L:2651902-2652022 9.99e-01 120 chrX:17293543-17293663 8.82e-01 120 chrX:9119424-9119544 9.59e-01 120 chr2L:12542120-12542240 1.00e+00 120 chrX:14743902-14744022 9.87e-01 120 chr3L:5926088-5926208 9.36e-01 120 chr2L:9235652-9235772 6.98e-01 120 chr3R:19627920-19628040 9.79e-01 120 chr3R:23969549-23969669 9.78e-01 120 chr3L:15034475-15034595 1.27e-02 120 chrX:3399389-3399509 5.31e-01 120 chr3L:12271462-12271582 1.48e-02 83_[+4(5.64e-05)]_29 chr2R:12547649-12547769 9.04e-01 120 chr3L:7592231-7592351 5.49e-01 120 chr3R:9237935-9238055 5.64e-01 120 chrX:16834358-16834478 9.54e-01 120 chr3R:28676998-28677118 4.32e-01 120 chr3L:18030015-18030135 7.51e-01 120 chr3L:18272435-18272555 8.87e-01 120 chrX:8677559-8677679 4.52e-01 120 chr2R:12035181-12035301 4.52e-03 120 chr2L:3880230-3880350 9.99e-01 120 chrX:14679305-14679425 9.27e-01 120 chrX:7703369-7703489 1.86e-01 120 chr2L:10760735-10760855 9.95e-01 120 chr3L:3437279-3437399 1.00e+00 120 chr3L:10767326-10767446 9.94e-01 120 chr2L:19930253-19930373 1.52e-01 120 chrX:8542115-8542235 1.07e-01 120 chr2R:11809470-11809590 1.25e-02 9_[+3(2.57e-06)]_103 chr2L:7871930-7872050 1.89e-01 120 chrX:16930474-16930594 7.81e-01 120 chr2R:10123662-10123782 2.18e-01 120 chr3R:16223765-16223885 9.95e-01 120 chr3R:10520688-10520808 1.81e-01 120 chrX:16103563-16103683 8.39e-02 120 chrX:1270775-1270895 3.13e-01 120 chr3L:16202724-16202844 6.87e-01 120 chrX:8444947-8445067 9.94e-01 120 chrX:13764540-13764660 5.54e-03 95_[+5(7.30e-05)]_17 chr3L:797030-797150 2.04e-01 120 chrX:9120973-9121093 9.88e-01 120 chr3L:18782219-18782339 9.98e-01 120 chr3R:21993044-21993164 5.26e-01 120 chr3R:26117830-26117950 8.70e-01 120 chrX:18899960-18900080 9.17e-01 120 chrX:10825474-10825594 7.28e-01 120 chr2R:10854275-10854395 8.30e-02 120 chr2L:21149217-21149337 3.05e-05 78_[+2(6.47e-07)]_34 chrX:12925973-12926093 3.86e-01 120 chrX:9899803-9899923 2.61e-01 120 chr2L:15908601-15908721 9.91e-01 120 chr3L:5554505-5554625 9.85e-01 120 chr2L:8894386-8894506 1.97e-02 120 chrX:16944149-16944269 5.49e-01 120 chr2R:11601954-11602074 7.35e-01 120 chr3R:11852077-11852197 9.91e-01 120 chr3R:25168354-25168474 4.39e-01 106_[+5(7.30e-05)]_6 chr2R:16097052-16097172 3.59e-01 120 chr3L:22471687-22471807 7.15e-01 120 chrX:2396635-2396755 6.87e-01 120 chr3L:15691331-15691451 9.17e-01 120 chr2L:7395908-7396028 9.72e-01 120 chr3L:14363260-14363380 8.94e-01 120 chr2L:1207597-1207717 8.19e-01 120 chr3R:18393588-18393708 9.87e-01 120 chr2L:19517415-19517535 6.50e-01 120 chr2R:7054309-7054429 1.43e-01 120 chrX:4262809-4262929 1.88e-01 120 chrX:16854865-16854985 9.17e-01 120 chrX:2011727-2011847 1.68e-01 120 chr2R:7254319-7254439 6.17e-01 120 chr2L:9493408-9493528 9.89e-01 120 chr2L:15442301-15442421 2.25e-01 120 chr2L:8982713-8982833 4.90e-01 120 chr2R:12772801-12772921 9.86e-01 120 chr2L:19140991-19141111 1.37e-01 120 chr3L:15592662-15592782 9.48e-01 120 chr2R:15034876-15034996 3.09e-01 120 chr3R:26012956-26013076 9.54e-01 120 chr2R:19860399-19860519 1.47e-02 120 chr3R:8955033-8955153 3.90e-01 120 chr2L:21096500-21096620 9.99e-01 120 chr3R:12720113-12720233 7.31e-02 120 chr3R:14875713-14875833 6.91e-01 120 chr3L:8951128-8951248 4.06e-01 112_[+5(7.30e-05)] chr3L:13923456-13923576 1.00e+00 120 chrX:10628972-10629092 1.00e+00 120 chrX:10387790-10387910 2.11e-04 23_[+4(1.30e-06)]_89 chr2R:10077914-10078034 9.47e-01 120 chrX:14169195-14169315 9.54e-01 120 chr3L:9691276-9691396 2.29e-01 89_[+3(7.78e-05)]_23 chr3L:554722-554842 1.00e+00 120 chrX:3690733-3690853 8.10e-01 120 chr3R:8867848-8867968 9.94e-01 120 chr2R:13008285-13008405 8.22e-01 120 chrX:6375802-6375922 9.38e-02 120 chr3R:26444254-26444374 9.99e-01 120 chrX:16650541-16650661 1.26e-02 4_[+4(5.64e-05)]_108 chrX:15297183-15297303 1.00e+00 120 chr3R:21493684-21493804 8.43e-01 120 chr3R:17535310-17535430 9.99e-01 120 chr3L:6157739-6157859 6.02e-02 120 chr3L:13905658-13905778 5.95e-01 120 chr2L:20759934-20760054 3.32e-01 120 chr3R:11661872-11661992 6.51e-01 120 chr3L:10745678-10745798 9.79e-01 120 chr2L:2905204-2905324 1.96e-01 107_[+3(7.78e-05)]_5 chr3R:18311392-18311512 1.00e+00 120 chr2L:7270411-7270531 3.11e-01 120 chr3R:26888428-26888548 6.04e-02 120 chr2R:11435202-11435322 8.00e-03 85_[+5(1.84e-06)]_27 chr3R:24010986-24011106 1.18e-02 120 chrX:21322736-21322856 9.62e-01 120 chr3R:25445643-25445763 1.00e+00 120 chr2L:7957102-7957222 9.94e-01 120 chrX:15384097-15384217 3.62e-01 120 chr2R:15240263-15240383 8.08e-02 101_[+4(5.64e-05)]_11 chr3L:7861180-7861300 9.90e-01 120 chrX:13274596-13274716 9.25e-01 120 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (5) found. ******************************************************************************** CPU: c27n09.farnam.hpc.yale.internal ********************************************************************************