******************************************************************************** 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/Oli.fasta CONTROL SEQUENCES= --none-- ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ chr3R:24206165-24206285 1.0000 120 chr3L:18795568-18795688 1.0000 120 chr3R:27426876-27426996 1.0000 120 chr3L:10428858-10428978 1.0000 120 chr2R:12229707-12229827 1.0000 120 chr2R:18564372-18564492 1.0000 120 chr3L:10337755-10337875 1.0000 120 chr3L:7862809-7862929 1.0000 120 chr2L:17583099-17583219 1.0000 120 chr3L:18789320-18789440 1.0000 120 chr3R:21613011-21613131 1.0000 120 chr3L:16289247-16289367 1.0000 120 chr3R:11663618-11663738 1.0000 120 chr3R:28327291-28327411 1.0000 120 chr3R:6352970-6353090 1.0000 120 chr2R:15134289-15134409 1.0000 120 chr2L:17589933-17590053 1.0000 120 chr3L:14328532-14328652 1.0000 120 chr2R:23187301-23187421 1.0000 120 chr2L:14024855-14024975 1.0000 120 chr3L:11278925-11279045 1.0000 120 chrX:5989511-5989631 1.0000 120 chr3R:10274973-10275093 1.0000 120 chr3R:10154418-10154538 1.0000 120 chr3L:10391093-10391213 1.0000 120 chr2R:14485493-14485613 1.0000 120 chr2L:1214613-1214733 1.0000 120 chrX:14634889-14635009 1.0000 120 chr3L:21056393-21056513 1.0000 120 chr2L:19252534-19252654 1.0000 120 chrX:3019742-3019862 1.0000 120 chr3L:10428222-10428342 1.0000 120 chr3L:16054267-16054387 1.0000 120 chr3R:22220959-22221079 1.0000 120 chr3R:15927247-15927367 1.0000 120 chr3R:13986793-13986913 1.0000 120 chrX:18533362-18533482 1.0000 120 chr3R:23396643-23396763 1.0000 120 chr3R:28623759-28623879 1.0000 120 chr2L:7492064-7492184 1.0000 120 chrX:11846457-11846577 1.0000 120 chrX:8206045-8206165 1.0000 120 chrX:3109004-3109124 1.0000 120 chr2L:6540142-6540262 1.0000 120 chr3R:24007858-24007978 1.0000 120 chr2L:17588716-17588836 1.0000 120 chrX:10718027-10718147 1.0000 120 chrX:3288974-3289094 1.0000 120 chr3L:3078550-3078670 1.0000 120 chr2R:18273479-18273599 1.0000 120 chrX:17780423-17780543 1.0000 120 chrX:3455605-3455725 1.0000 120 chrX:17187620-17187740 1.0000 120 chr2R:11803324-11803444 1.0000 120 chr3L:6157700-6157820 1.0000 120 chr3L:3786901-3787021 1.0000 120 chr3R:16769557-16769677 1.0000 120 chr3L:6817084-6817204 1.0000 120 chr3R:22878547-22878667 1.0000 120 chr2L:3435185-3435305 1.0000 120 chrX:6542453-6542573 1.0000 120 chr2R:22384463-22384583 1.0000 120 chr2L:13876785-13876905 1.0000 120 chr3R:23067510-23067630 1.0000 120 chr3R:12451498-12451618 1.0000 120 chr3R:15129126-15129246 1.0000 120 chr3L:18782216-18782336 1.0000 120 chr3L:5188486-5188606 1.0000 120 chr2L:8552598-8552718 1.0000 120 chr3R:16215121-16215241 1.0000 120 chr2L:3805306-3805426 1.0000 120 chr2R:11176277-11176397 1.0000 120 chrX:11441054-11441174 1.0000 120 chr3L:16657032-16657152 1.0000 120 chr3L:19338421-19338541 1.0000 120 chrX:10573667-10573787 1.0000 120 chr3L:16697225-16697345 1.0000 120 chrX:3714162-3714282 1.0000 120 chrX:19106974-19107094 1.0000 120 chr2R:14915125-14915245 1.0000 120 chr2L:11394249-11394369 1.0000 120 chr2L:16869043-16869163 1.0000 120 chr3R:13549648-13549768 1.0000 120 chr3R:18438891-18439011 1.0000 120 chr3R:13892996-13893116 1.0000 120 chr3R:21594513-21594633 1.0000 120 chr3L:4000820-4000940 1.0000 120 chr2L:7150930-7151050 1.0000 120 chr2L:5610220-5610340 1.0000 120 chr3R:9494366-9494486 1.0000 120 chr3L:21859841-21859961 1.0000 120 chrX:12724783-12724903 1.0000 120 chr2R:10854317-10854437 1.0000 120 chr2R:10194958-10195078 1.0000 120 chr2R:20126689-20126809 1.0000 120 chr3L:16482295-16482415 1.0000 120 chr3R:28904289-28904409 1.0000 120 chr2R:8734604-8734724 1.0000 120 chrX:12249024-12249144 1.0000 120 chr3L:17532344-17532464 1.0000 120 chr3R:15117850-15117970 1.0000 120 chr3L:15275544-15275664 1.0000 120 chr3L:3449891-3450011 1.0000 120 chr3R:8784948-8785068 1.0000 120 chrX:20644120-20644240 1.0000 120 chr2L:21096448-21096568 1.0000 120 chr3R:10648912-10649032 1.0000 120 chr2L:13512218-13512338 1.0000 120 chr3R:8469851-8469971 1.0000 120 chr2R:11602031-11602151 1.0000 120 chr2R:7241756-7241876 1.0000 120 chr3R:9888839-9888959 1.0000 120 chrX:11885495-11885615 1.0000 120 chrX:19964388-19964508 1.0000 120 chr2R:23668867-23668987 1.0000 120 chr3L:5926070-5926190 1.0000 120 chr3R:16241929-16242049 1.0000 120 chr2L:18566852-18566972 1.0000 120 chr2R:24893676-24893796 1.0000 120 chrX:16854875-16854995 1.0000 120 chr3R:14386100-14386220 1.0000 120 chr3R:14284574-14284694 1.0000 120 chr2R:12547682-12547802 1.0000 120 chr2L:3851434-3851554 1.0000 120 chr2R:14305329-14305449 1.0000 120 chr3L:775073-775193 1.0000 120 chr3L:16544357-16544477 1.0000 120 chrX:11848750-11848870 1.0000 120 chr3R:15139513-15139633 1.0000 120 chrX:19166452-19166572 1.0000 120 chr3L:11429843-11429963 1.0000 120 chr3L:17404813-17404933 1.0000 120 chrX:8125362-8125482 1.0000 120 chr3L:8951074-8951194 1.0000 120 chr3R:26892920-26893040 1.0000 120 chrX:17782135-17782255 1.0000 120 chrX:2396671-2396791 1.0000 120 chr2L:14441048-14441168 1.0000 120 chr3L:2845321-2845441 1.0000 120 chrX:13109881-13110001 1.0000 120 chr3L:16452468-16452588 1.0000 120 chr3R:30812562-30812682 1.0000 120 chr2R:15351246-15351366 1.0000 120 chrX:13226593-13226713 1.0000 120 chr2L:9564657-9564777 1.0000 120 chr2R:15034855-15034975 1.0000 120 chr2L:18648380-18648500 1.0000 120 chr2R:6157426-6157546 1.0000 120 chr3L:19074029-19074149 1.0000 120 chr2L:20889938-20890058 1.0000 120 chr2R:9681851-9681971 1.0000 120 chr3L:3814656-3814776 1.0000 120 chr3R:11661872-11661992 1.0000 120 chrX:13789082-13789202 1.0000 120 chr2L:17588917-17589037 1.0000 120 chr3L:16760408-16760528 1.0000 120 chr2L:14245592-14245712 1.0000 120 chrX:14743936-14744056 1.0000 120 chr3R:21112525-21112645 1.0000 120 chrX:18921059-18921179 1.0000 120 chrX:16580103-16580223 1.0000 120 chr2L:7871941-7872061 1.0000 120 chr3L:18114150-18114270 1.0000 120 chrX:16834368-16834488 1.0000 120 chr2R:13261850-13261970 1.0000 120 chr3L:22277379-22277499 1.0000 120 chr2R:8045119-8045239 1.0000 120 chr3R:14095521-14095641 1.0000 120 chr2R:17533765-17533885 1.0000 120 chr3L:15693194-15693314 1.0000 120 chr3R:14470754-14470874 1.0000 120 chr2R:23578532-23578652 1.0000 120 chr3L:13356164-13356284 1.0000 120 chr3L:11291568-11291688 1.0000 120 chr3R:6760825-6760945 1.0000 120 chr2L:15908549-15908669 1.0000 120 chrX:9899841-9899961 1.0000 120 chr2R:11176480-11176600 1.0000 120 chr3L:10893508-10893628 1.0000 120 chr3R:26014366-26014486 1.0000 120 chr3L:18402711-18402831 1.0000 120 chr3R:11852061-11852181 1.0000 120 chrX:10825456-10825576 1.0000 120 chr3L:14172698-14172818 1.0000 120 chr3L:9028206-9028326 1.0000 120 chr3R:19113985-19114105 1.0000 120 chr3R:25445632-25445752 1.0000 120 chrX:14840652-14840772 1.0000 120 chrX:17330407-17330527 1.0000 120 chrX:11081385-11081505 1.0000 120 chr3R:23921818-23921938 1.0000 120 chr2L:11331770-11331890 1.0000 120 chrX:20631285-20631405 1.0000 120 chr3L:11303985-11304105 1.0000 120 chr3R:30305012-30305132 1.0000 120 chr3L:20471091-20471211 1.0000 120 chr2R:19860420-19860540 1.0000 120 chrX:18524980-18525100 1.0000 120 chr3R:26121901-26122021 1.0000 120 chr3R:19165077-19165197 1.0000 120 chr3R:26436689-26436809 1.0000 120 chr3R:26117765-26117885 1.0000 120 chr3R:9344872-9344992 1.0000 120 chr2R:14971103-14971223 1.0000 120 chr3R:10520631-10520751 1.0000 120 chr3R:26937641-26937761 1.0000 120 chr2L:10543533-10543653 1.0000 120 chr3L:8692045-8692165 1.0000 120 chr2R:12727627-12727747 1.0000 120 chrX:947635-947755 1.0000 120 chr3L:20517038-20517158 1.0000 120 chr2R:7987802-7987922 1.0000 120 chr3L:8751409-8751529 1.0000 120 chr2R:15240250-15240370 1.0000 120 chrX:19225171-19225291 1.0000 120 chr3L:10745741-10745861 1.0000 120 chr2R:18994164-18994284 1.0000 120 chr3L:3855314-3855434 1.0000 120 chr2R:16096938-16097058 1.0000 120 chr2L:7957308-7957428 1.0000 120 chr2L:8554452-8554572 1.0000 120 chr2L:18377288-18377408 1.0000 120 chrX:8444931-8445051 1.0000 120 chr3L:14363292-14363412 1.0000 120 chr3R:8744320-8744440 1.0000 120 chr2R:14576034-14576154 1.0000 120 chr3L:3875181-3875301 1.0000 120 chr3L:824617-824737 1.0000 120 chr2L:7957089-7957209 1.0000 120 chrX:5783796-5783916 1.0000 120 chr3L:20630729-20630849 1.0000 120 chr2R:11275834-11275954 1.0000 120 chr3R:8171641-8171761 1.0000 120 chr3R:8960450-8960570 1.0000 120 chrX:9352839-9352959 1.0000 120 chrX:20507884-20508004 1.0000 120 chr3L:15592724-15592844 1.0000 120 chr2R:13429214-13429334 1.0000 120 chr3R:8867869-8867989 1.0000 120 chrX:10067675-10067795 1.0000 120 chr3R:22121347-22121467 1.0000 120 chr3L:7783456-7783576 1.0000 120 chr3R:28676976-28677096 1.0000 120 chr3L:18782419-18782539 1.0000 120 chrX:9202191-9202311 1.0000 120 chr3L:18784699-18784819 1.0000 120 chrX:19009015-19009135 1.0000 120 chr2L:8982707-8982827 1.0000 120 chr2L:9206558-9206678 1.0000 120 chr3R:26888450-26888570 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_Oli/ -dna -nmotifs 5 -w 8 -maxsize 250000 -nostatus ../result/final_prediction/fly/fasta/RankLinear8.0_60/Oli.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 0.359 C 0.144 G 0.143 T 0.354 Background letter frequencies (from file dataset with add-one prior applied): A 0.359 C 0.144 G 0.143 T 0.354 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF GGGCGGSM MEME-1 width = 8 sites = 2 llr = 27 E-value = 1.5e+004 ******************************************************************************** -------------------------------------------------------------------------------- Motif GGGCGGSM MEME-1 Description -------------------------------------------------------------------------------- Simplified A :::::::5 pos.-specific C :::a::55 probability G aaa:aa5: matrix T :::::::: bits 2.8 ****** 2.5 ****** 2.2 ****** 2.0 ****** Relative 1.7 ******* Entropy 1.4 ******* (19.8 bits) 1.1 ******** 0.8 ******** 0.6 ******** 0.3 ******** 0.0 -------- Multilevel GGGCGGCA consensus GC sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGGCGGSM MEME-1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr3L:18784699-18784819 62 3.56e-07 tttttcatac gggcggcc accccttttc chr2R:15034855-15034975 68 1.24e-06 AGTCGAAGCT GGGCGGGA ATTATCTATC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGGCGGSM MEME-1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr3L:18784699-18784819 3.6e-07 61_[+1]_51 chr2R:15034855-15034975 1.2e-06 67_[+1]_45 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGGCGGSM MEME-1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF GGGCGGSM width=8 seqs=2 chr3L:18784699-18784819 ( 62) GGGCGGCC 1 chr2R:15034855-15034975 ( 68) GGGCGGGA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGGCGGSM MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 28250 bayes= 13.7859 E= 1.5e+004 -765 -765 280 -765 -765 -765 280 -765 -765 -765 280 -765 -765 279 -765 -765 -765 -765 280 -765 -765 -765 280 -765 -765 179 180 -765 47 179 -765 -765 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGGCGGSM MEME-1 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 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.500000 0.500000 0.000000 0.500000 0.500000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGGCGGSM MEME-1 regular expression -------------------------------------------------------------------------------- GGGCGG[CG][AC] -------------------------------------------------------------------------------- Time 7.53 secs. ******************************************************************************** ******************************************************************************** MOTIF GCGCGCCM MEME-2 width = 8 sites = 2 llr = 29 E-value = 1.8e+004 ******************************************************************************** -------------------------------------------------------------------------------- Motif GCGCGCCM MEME-2 Description -------------------------------------------------------------------------------- Simplified A :::::::5 pos.-specific C :a:a:aa5 probability G a:a:a::: matrix T :::::::: bits 2.8 ******* 2.5 ******* 2.2 ******* 2.0 ******* Relative 1.7 ******* Entropy 1.4 ******* (20.7 bits) 1.1 ******** 0.8 ******** 0.6 ******** 0.3 ******** 0.0 -------- Multilevel GCGCGCCA consensus C sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCGCGCCM MEME-2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr2L:7957308-7957428 63 1.81e-07 TTTTCAGTCT GCGCGCCC AGTGTCAGTG chr3R:16215121-16215241 81 6.32e-07 TACTGACTGA GCGCGCCA AAAAGTAGGC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCGCGCCM MEME-2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr2L:7957308-7957428 1.8e-07 62_[+2]_50 chr3R:16215121-16215241 6.3e-07 80_[+2]_32 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCGCGCCM MEME-2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF GCGCGCCM width=8 seqs=2 chr2L:7957308-7957428 ( 63) GCGCGCCC 1 chr3R:16215121-16215241 ( 81) GCGCGCCA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCGCGCCM MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 28250 bayes= 13.7859 E= 1.8e+004 -765 -765 280 -765 -765 279 -765 -765 -765 -765 280 -765 -765 279 -765 -765 -765 -765 280 -765 -765 279 -765 -765 -765 279 -765 -765 47 179 -765 -765 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCGCGCCM MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 2 E= 1.8e+004 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.500000 0.500000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCGCGCCM MEME-2 regular expression -------------------------------------------------------------------------------- GCGCGCC[AC] -------------------------------------------------------------------------------- Time 13.90 secs. ******************************************************************************** ******************************************************************************** MOTIF CACTGCSA MEME-3 width = 8 sites = 13 llr = 132 E-value = 1.1e+004 ******************************************************************************** -------------------------------------------------------------------------------- Motif CACTGCSA MEME-3 Description -------------------------------------------------------------------------------- Simplified A :7:::::8 pos.-specific C 71a2:a5: probability G 32::a:52 matrix T :1:8:::: bits 2.8 * ** 2.5 * ** 2.2 * ** 2.0 * * ** Relative 1.7 * * *** Entropy 1.4 * * *** (14.7 bits) 1.1 * ****** 0.8 * ****** 0.6 ******** 0.3 ******** 0.0 -------- Multilevel CACTGCCA consensus G G sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CACTGCSA MEME-3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr3R:10154418-10154538 110 2.81e-06 TTAGAACTGA CACTGCCA ATG chr3L:7862809-7862929 101 2.81e-06 ACATCATACT CACTGCCA ATTTTTGTAA chr3L:7783456-7783576 34 5.59e-06 TTTTTGCCTA CACTGCGA AGAAGTAGAG chr2R:15134289-15134409 113 5.59e-06 TTGACTGCTG CACTGCGA chr3L:3449891-3450011 89 6.71e-06 CTTTTTTAAG CGCTGCCA ATAATGCCAA chr3R:10648912-10649032 46 1.29e-05 TTCAGTAGGT CACCGCCA ATTAACTCAA chr3L:22277379-22277499 65 1.79e-05 GTTGGCCAAA GACTGCGA CCTAACTGCT chrX:16580103-16580223 29 1.79e-05 AATCCGAATT CACTGCGG AAGATGCCCT chr3R:15139513-15139633 16 1.79e-05 atggttgtac gactgcga attttgaaaa chr3R:26117765-26117885 16 2.21e-05 AAATGTGAGT CCCTGCGA AAGTAAGAAA chr3R:22220959-22221079 110 2.68e-05 CTACTTATAT GACCGCCA CTG chrX:13789082-13789202 24 3.43e-05 AAGCAAAATA CTCTGCCA TACTCTGGTA chr2L:20889938-20890058 46 3.74e-05 TGCGATTTAA GGCTGCCG CAGGTGCACC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CACTGCSA MEME-3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr3R:10154418-10154538 2.8e-06 109_[+3]_3 chr3L:7862809-7862929 2.8e-06 100_[+3]_12 chr3L:7783456-7783576 5.6e-06 33_[+3]_79 chr2R:15134289-15134409 5.6e-06 112_[+3] chr3L:3449891-3450011 6.7e-06 88_[+3]_24 chr3R:10648912-10649032 1.3e-05 45_[+3]_67 chr3L:22277379-22277499 1.8e-05 64_[+3]_48 chrX:16580103-16580223 1.8e-05 28_[+3]_84 chr3R:15139513-15139633 1.8e-05 15_[+3]_97 chr3R:26117765-26117885 2.2e-05 15_[+3]_97 chr3R:22220959-22221079 2.7e-05 109_[+3]_3 chrX:13789082-13789202 3.4e-05 23_[+3]_89 chr2L:20889938-20890058 3.7e-05 45_[+3]_67 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CACTGCSA MEME-3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF CACTGCSA width=8 seqs=13 chr3R:10154418-10154538 ( 110) CACTGCCA 1 chr3L:7862809-7862929 ( 101) CACTGCCA 1 chr3L:7783456-7783576 ( 34) CACTGCGA 1 chr2R:15134289-15134409 ( 113) CACTGCGA 1 chr3L:3449891-3450011 ( 89) CGCTGCCA 1 chr3R:10648912-10649032 ( 46) CACCGCCA 1 chr3L:22277379-22277499 ( 65) GACTGCGA 1 chrX:16580103-16580223 ( 29) CACTGCGG 1 chr3R:15139513-15139633 ( 16) GACTGCGA 1 chr3R:26117765-26117885 ( 16) CCCTGCGA 1 chr3R:22220959-22221079 ( 110) GACCGCCA 1 chrX:13789082-13789202 ( 24) CTCTGCCA 1 chr2L:20889938-20890058 ( 46) GGCTGCCG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CACTGCSA MEME-3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 28250 bayes= 11.6156 E= 1.1e+004 -1035 226 111 -1035 95 -90 11 -220 -1035 279 -1035 -1035 -1035 9 -1035 126 -1035 -1035 281 -1035 -1035 279 -1035 -1035 -1035 190 169 -1035 124 -1035 11 -1035 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CACTGCSA MEME-3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 13 E= 1.1e+004 0.000000 0.692308 0.307692 0.000000 0.692308 0.076923 0.153846 0.076923 0.000000 1.000000 0.000000 0.000000 0.000000 0.153846 0.000000 0.846154 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.538462 0.461538 0.000000 0.846154 0.000000 0.153846 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CACTGCSA MEME-3 regular expression -------------------------------------------------------------------------------- [CG]ACTGC[CG]A -------------------------------------------------------------------------------- Time 20.15 secs. ******************************************************************************** ******************************************************************************** MOTIF CGTGGSAC MEME-4 width = 8 sites = 3 llr = 39 E-value = 1.7e+004 ******************************************************************************** -------------------------------------------------------------------------------- Motif CGTGGSAC MEME-4 Description -------------------------------------------------------------------------------- Simplified A ::::::a: pos.-specific C a::::7:a probability G :a:aa3:: matrix T ::a::::: bits 2.8 ** ** * 2.5 ** ** * 2.2 ** ** * 2.0 ** *** * Relative 1.7 ** *** * Entropy 1.4 ******** (18.9 bits) 1.1 ******** 0.8 ******** 0.6 ******** 0.3 ******** 0.0 -------- Multilevel CGTGGCAC consensus G sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CGTGGSAC MEME-4 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr3L:8751409-8751529 90 1.11e-06 TTTTTCTATA CGTGGCAC AATGGAATTG chr3R:23921818-23921938 12 1.11e-06 AATTAATTTA CGTGGCAC AACATTTGAC chr3L:15693194-15693314 78 2.21e-06 TTAGATTAAA CGTGGGAC TAAACTTTTT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CGTGGSAC MEME-4 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr3L:8751409-8751529 1.1e-06 89_[+4]_23 chr3R:23921818-23921938 1.1e-06 11_[+4]_101 chr3L:15693194-15693314 2.2e-06 77_[+4]_35 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CGTGGSAC MEME-4 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF CGTGGSAC width=8 seqs=3 chr3L:8751409-8751529 ( 90) CGTGGCAC 1 chr3R:23921818-23921938 ( 12) CGTGGCAC 1 chr3L:15693194-15693314 ( 78) CGTGGGAC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CGTGGSAC MEME-4 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 28250 bayes= 12.8598 E= 1.7e+004 -823 279 -823 -823 -823 -823 280 -823 -823 -823 -823 150 -823 -823 280 -823 -823 -823 280 -823 -823 221 122 -823 147 -823 -823 -823 -823 279 -823 -823 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CGTGGSAC MEME-4 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 3 E= 1.7e+004 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 0.000000 0.000000 1.000000 0.000000 0.000000 0.666667 0.333333 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CGTGGSAC MEME-4 regular expression -------------------------------------------------------------------------------- CGTGG[CG]AC -------------------------------------------------------------------------------- Time 26.35 secs. ******************************************************************************** ******************************************************************************** MOTIF GGCGTAGC MEME-5 width = 8 sites = 2 llr = 27 E-value = 2.2e+004 ******************************************************************************** -------------------------------------------------------------------------------- Motif GGCGTAGC MEME-5 Description -------------------------------------------------------------------------------- Simplified A :::::a:: pos.-specific C ::a::::a probability G aa:a::a: matrix T ::::a::: bits 2.8 **** ** 2.5 **** ** 2.2 **** ** 2.0 **** ** Relative 1.7 **** ** Entropy 1.4 ******** (19.8 bits) 1.1 ******** 0.8 ******** 0.6 ******** 0.3 ******** 0.0 -------- Multilevel GGCGTAGC consensus sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGCGTAGC MEME-5 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr3R:28676976-28677096 16 1.10e-06 CGCATACAAG GGCGTAGC AACTGAAATA chr2L:16869043-16869163 6 1.10e-06 AGAAA GGCGTAGC CCTTACACAC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGCGTAGC MEME-5 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr3R:28676976-28677096 1.1e-06 15_[+5]_97 chr2L:16869043-16869163 1.1e-06 5_[+5]_107 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGCGTAGC MEME-5 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF GGCGTAGC width=8 seqs=2 chr3R:28676976-28677096 ( 16) GGCGTAGC 1 chr2L:16869043-16869163 ( 6) GGCGTAGC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGCGTAGC MEME-5 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 28250 bayes= 13.7859 E= 2.2e+004 -765 -765 280 -765 -765 -765 280 -765 -765 279 -765 -765 -765 -765 280 -765 -765 -765 -765 149 147 -765 -765 -765 -765 -765 280 -765 -765 279 -765 -765 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGCGTAGC MEME-5 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 2 E= 2.2e+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 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGCGTAGC MEME-5 regular expression -------------------------------------------------------------------------------- GGCGTAGC -------------------------------------------------------------------------------- Time 32.55 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr3R:24206165-24206285 1.12e-01 120 chr3L:18795568-18795688 9.98e-01 120 chr3R:27426876-27426996 9.96e-01 120 chr3L:10428858-10428978 9.87e-01 120 chr2R:12229707-12229827 2.24e-01 120 chr2R:18564372-18564492 9.79e-01 120 chr3L:10337755-10337875 5.05e-01 120 chr3L:7862809-7862929 6.33e-03 100_[+3(2.81e-06)]_12 chr2L:17583099-17583219 4.34e-01 120 chr3L:18789320-18789440 1.00e+00 120 chr3R:21613011-21613131 9.60e-01 120 chr3L:16289247-16289367 6.12e-02 120 chr3R:11663618-11663738 9.96e-01 120 chr3R:28327291-28327411 7.56e-01 120 chr3R:6352970-6353090 2.02e-01 120 chr2R:15134289-15134409 2.79e-03 112_[+3(5.59e-06)] chr2L:17589933-17590053 6.31e-01 120 chr3L:14328532-14328652 7.35e-01 120 chr2R:23187301-23187421 9.26e-01 120 chr2L:14024855-14024975 1.00e+00 120 chr3L:11278925-11279045 9.67e-01 120 chrX:5989511-5989631 9.81e-01 120 chr3R:10274973-10275093 8.46e-01 120 chr3R:10154418-10154538 1.61e-02 109_[+3(2.81e-06)]_3 chr3L:10391093-10391213 9.82e-01 120 chr2R:14485493-14485613 8.41e-01 120 chr2L:1214613-1214733 8.91e-01 120 chrX:14634889-14635009 8.06e-01 120 chr3L:21056393-21056513 3.39e-01 120 chr2L:19252534-19252654 2.67e-01 120 chrX:3019742-3019862 9.35e-01 120 chr3L:10428222-10428342 9.86e-01 120 chr3L:16054267-16054387 9.95e-01 120 chr3R:22220959-22221079 1.28e-02 109_[+3(2.68e-05)]_3 chr3R:15927247-15927367 8.78e-01 120 chr3R:13986793-13986913 3.31e-02 120 chrX:18533362-18533482 1.83e-01 [+4(4.88e-05)]_112 chr3R:23396643-23396763 9.36e-01 120 chr3R:28623759-28623879 9.84e-01 120 chr2L:7492064-7492184 2.73e-01 120 chrX:11846457-11846577 6.05e-01 120 chrX:8206045-8206165 9.99e-01 120 chrX:3109004-3109124 4.29e-01 120 chr2L:6540142-6540262 1.44e-03 120 chr3R:24007858-24007978 8.01e-01 120 chr2L:17588716-17588836 9.95e-01 120 chrX:10718027-10718147 7.07e-01 120 chrX:3288974-3289094 6.98e-02 120 chr3L:3078550-3078670 7.01e-01 120 chr2R:18273479-18273599 9.01e-01 120 chrX:17780423-17780543 1.27e-03 21_[+3(9.06e-05)]_71_[+2(5.38e-05)]_\ 12 chrX:3455605-3455725 2.75e-01 120 chrX:17187620-17187740 8.73e-02 8_[+4(8.17e-05)]_104 chr2R:11803324-11803444 7.33e-01 120 chr3L:6157700-6157820 7.46e-01 120 chr3L:3786901-3787021 4.22e-01 120 chr3R:16769557-16769677 7.46e-01 120 chr3L:6817084-6817204 8.55e-01 120 chr3R:22878547-22878667 9.40e-01 120 chr2L:3435185-3435305 4.88e-01 120 chrX:6542453-6542573 9.95e-01 120 chr2R:22384463-22384583 1.80e-03 120 chr2L:13876785-13876905 9.52e-01 120 chr3R:23067510-23067630 9.99e-01 120 chr3R:12451498-12451618 4.59e-01 120 chr3R:15129126-15129246 2.46e-02 19_[+1(5.02e-05)]_93 chr3L:18782216-18782336 9.57e-01 120 chr3L:5188486-5188606 3.28e-01 120 chr2L:8552598-8552718 9.96e-01 120 chr3R:16215121-16215241 1.03e-04 80_[+2(6.32e-07)]_32 chr2L:3805306-3805426 6.21e-02 16_[+1(5.02e-05)]_96 chr2R:11176277-11176397 9.55e-01 120 chrX:11441054-11441174 9.00e-02 120 chr3L:16657032-16657152 4.24e-01 120 chr3L:19338421-19338541 9.73e-01 120 chrX:10573667-10573787 3.92e-01 120 chr3L:16697225-16697345 1.14e-01 120 chrX:3714162-3714282 9.71e-01 120 chrX:19106974-19107094 3.63e-02 120 chr2R:14915125-14915245 9.22e-01 120 chr2L:11394249-11394369 9.11e-01 120 chr2L:16869043-16869163 4.93e-05 5_[+5(1.10e-06)]_107 chr3R:13549648-13549768 9.92e-01 120 chr3R:18438891-18439011 5.20e-01 120 chr3R:13892996-13893116 6.41e-01 120 chr3R:21594513-21594633 2.72e-01 120 chr3L:4000820-4000940 6.68e-01 120 chr2L:7150930-7151050 9.93e-01 120 chr2L:5610220-5610340 2.20e-01 120 chr3R:9494366-9494486 1.00e+00 120 chr3L:21859841-21859961 7.88e-01 120 chrX:12724783-12724903 6.25e-01 120 chr2R:10854317-10854437 6.69e-01 120 chr2R:10194958-10195078 9.20e-01 120 chr2R:20126689-20126809 4.99e-01 120 chr3L:16482295-16482415 5.76e-01 120 chr3R:28904289-28904409 9.93e-01 120 chr2R:8734604-8734724 6.68e-01 120 chrX:12249024-12249144 9.84e-01 120 chr3L:17532344-17532464 8.99e-01 120 chr3R:15117850-15117970 8.60e-01 120 chr3L:15275544-15275664 9.87e-01 120 chr3L:3449891-3450011 8.74e-05 88_[+3(6.71e-06)]_24 chr3R:8784948-8785068 5.72e-01 120 chrX:20644120-20644240 3.76e-01 120 chr2L:21096448-21096568 8.55e-01 120 chr3R:10648912-10649032 4.89e-04 26_[+1(5.02e-05)]_11_[+3(1.29e-05)]_\ 67 chr2L:13512218-13512338 6.58e-01 120 chr3R:8469851-8469971 9.98e-01 120 chr2R:11602031-11602151 9.88e-01 120 chr2R:7241756-7241876 5.12e-01 120 chr3R:9888839-9888959 9.72e-01 120 chrX:11885495-11885615 3.28e-01 120 chrX:19964388-19964508 4.95e-01 120 chr2R:23668867-23668987 2.53e-04 65_[+2(8.82e-06)]_47 chr3L:5926070-5926190 7.16e-01 120 chr3R:16241929-16242049 9.33e-01 120 chr2L:18566852-18566972 9.91e-01 120 chr2R:24893676-24893796 1.31e-01 120 chrX:16854875-16854995 5.86e-01 120 chr3R:14386100-14386220 3.71e-03 120 chr3R:14284574-14284694 5.93e-02 120 chr2R:12547682-12547802 9.64e-01 120 chr2L:3851434-3851554 1.00e+00 120 chr2R:14305329-14305449 9.26e-01 120 chr3L:775073-775193 3.90e-02 87_[+4(8.17e-05)]_25 chr3L:16544357-16544477 3.48e-01 120 chrX:11848750-11848870 9.81e-01 120 chr3R:15139513-15139633 6.89e-02 15_[+3(1.79e-05)]_97 chrX:19166452-19166572 4.95e-01 120 chr3L:11429843-11429963 5.96e-01 120 chr3L:17404813-17404933 9.49e-01 120 chrX:8125362-8125482 1.00e+00 120 chr3L:8951074-8951194 9.70e-01 120 chr3R:26892920-26893040 8.10e-01 120 chrX:17782135-17782255 4.64e-01 120 chrX:2396671-2396791 4.56e-01 120 chr2L:14441048-14441168 1.00e-01 120 chr3L:2845321-2845441 9.36e-01 120 chrX:13109881-13110001 8.25e-01 120 chr3L:16452468-16452588 8.45e-01 120 chr3R:30812562-30812682 5.38e-01 120 chr2R:15351246-15351366 4.64e-01 120 chrX:13226593-13226713 9.76e-01 120 chr2L:9564657-9564777 9.74e-01 120 chr2R:15034855-15034975 5.42e-04 67_[+1(1.24e-06)]_45 chr2L:18648380-18648500 8.41e-01 120 chr2R:6157426-6157546 4.28e-01 120 chr3L:19074029-19074149 9.99e-01 120 chr2L:20889938-20890058 2.83e-03 45_[+3(3.74e-05)]_67 chr2R:9681851-9681971 7.11e-01 120 chr3L:3814656-3814776 2.06e-01 120 chr3R:11661872-11661992 5.73e-01 120 chrX:13789082-13789202 1.47e-01 23_[+3(3.43e-05)]_89 chr2L:17588917-17589037 9.96e-01 120 chr3L:16760408-16760528 2.27e-01 120 chr2L:14245592-14245712 2.44e-01 120 chrX:14743936-14744056 9.96e-01 120 chr3R:21112525-21112645 7.04e-01 120 chrX:18921059-18921179 9.98e-01 120 chrX:16580103-16580223 6.68e-02 28_[+3(1.79e-05)]_84 chr2L:7871941-7872061 6.71e-01 120 chr3L:18114150-18114270 8.61e-01 120 chrX:16834368-16834488 7.31e-01 120 chr2R:13261850-13261970 9.92e-01 120 chr3L:22277379-22277499 1.99e-02 64_[+3(1.79e-05)]_48 chr2R:8045119-8045239 7.19e-01 120 chr3R:14095521-14095641 7.79e-01 120 chr2R:17533765-17533885 8.95e-01 120 chr3L:15693194-15693314 4.66e-02 77_[+4(2.21e-06)]_35 chr3R:14470754-14470874 9.62e-01 120 chr2R:23578532-23578652 2.33e-01 120 chr3L:13356164-13356284 1.49e-01 120 chr3L:11291568-11291688 3.97e-01 120 chr3R:6760825-6760945 7.53e-01 120 chr2L:15908549-15908669 8.43e-01 120 chrX:9899841-9899961 7.34e-01 120 chr2R:11176480-11176600 7.31e-01 120 chr3L:10893508-10893628 1.00e+00 120 chr3R:26014366-26014486 8.22e-01 120 chr3L:18402711-18402831 9.10e-01 120 chr3R:11852061-11852181 5.13e-01 120 chrX:10825456-10825576 1.72e-01 120 chr3L:14172698-14172818 7.70e-01 120 chr3L:9028206-9028326 4.57e-01 120 chr3R:19113985-19114105 1.93e-01 120 chr3R:25445632-25445752 5.65e-01 120 chrX:14840652-14840772 1.00e+00 120 chrX:17330407-17330527 9.14e-01 120 chrX:11081385-11081505 1.80e-01 120 chr3R:23921818-23921938 8.94e-03 11_[+4(1.11e-06)]_101 chr2L:11331770-11331890 8.84e-01 120 chrX:20631285-20631405 9.95e-01 120 chr3L:11303985-11304105 1.84e-01 120 chr3R:30305012-30305132 8.54e-01 120 chr3L:20471091-20471211 5.53e-03 120 chr2R:19860420-19860540 4.64e-01 120 chrX:18524980-18525100 9.18e-01 120 chr3R:26121901-26122021 6.77e-02 120 chr3R:19165077-19165197 8.07e-01 120 chr3R:26436689-26436809 1.00e+00 120 chr3R:26117765-26117885 3.90e-02 15_[+3(2.21e-05)]_97 chr3R:9344872-9344992 3.03e-01 120 chr2R:14971103-14971223 4.36e-02 120 chr3R:10520631-10520751 9.84e-01 120 chr3R:26937641-26937761 1.74e-01 120 chr2L:10543533-10543653 9.62e-01 120 chr3L:8692045-8692165 3.79e-01 120 chr2R:12727627-12727747 9.94e-01 120 chrX:947635-947755 7.77e-01 120 chr3L:20517038-20517158 7.17e-01 120 chr2R:7987802-7987922 6.18e-01 120 chr3L:8751409-8751529 1.09e-02 89_[+4(1.11e-06)]_23 chr2R:15240250-15240370 6.21e-01 120 chrX:19225171-19225291 9.65e-01 120 chr3L:10745741-10745861 1.00e+00 120 chr2R:18994164-18994284 6.40e-01 120 chr3L:3855314-3855434 9.94e-01 120 chr2R:16096938-16097058 8.20e-01 120 chr2L:7957308-7957428 1.75e-05 62_[+2(1.81e-07)]_50 chr2L:8554452-8554572 5.82e-01 120 chr2L:18377288-18377408 8.81e-01 120 chrX:8444931-8445051 4.47e-01 120 chr3L:14363292-14363412 2.53e-01 120 chr3R:8744320-8744440 5.66e-01 120 chr2R:14576034-14576154 9.98e-01 120 chr3L:3875181-3875301 5.58e-01 120 chr3L:824617-824737 7.61e-01 120 chr2L:7957089-7957209 4.76e-01 120 chrX:5783796-5783916 4.18e-02 120 chr3L:20630729-20630849 1.58e-01 120 chr2R:11275834-11275954 6.05e-01 120 chr3R:8171641-8171761 2.77e-01 120 chr3R:8960450-8960570 9.74e-01 120 chrX:9352839-9352959 9.85e-01 120 chrX:20507884-20508004 1.72e-01 120 chr3L:15592724-15592844 9.25e-01 120 chr2R:13429214-13429334 4.51e-01 120 chr3R:8867869-8867989 1.00e+00 120 chrX:10067675-10067795 9.85e-02 120 chr3R:22121347-22121467 7.78e-01 120 chr3L:7783456-7783576 2.00e-02 33_[+3(5.59e-06)]_79 chr3R:28676976-28677096 4.53e-04 15_[+5(1.10e-06)]_97 chr3L:18782419-18782539 3.56e-01 120 chrX:9202191-9202311 1.00e+00 120 chr3L:18784699-18784819 2.86e-05 61_[+1(3.56e-07)]_51 chrX:19009015-19009135 1.22e-01 120 chr2L:8982707-8982827 9.97e-01 120 chr2L:9206558-9206678 9.95e-01 120 chr3R:26888450-26888570 4.22e-01 120 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (5) found. ******************************************************************************** CPU: c27n08.farnam.hpc.yale.internal ********************************************************************************