******************************************************************************** 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/pb.fasta CONTROL SEQUENCES= --none-- ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ chr3L:11370016-11370136 1.0000 120 chr3L:19349874-19349994 1.0000 120 chr2L:15249208-15249328 1.0000 120 chrX:2036986-2037106 1.0000 120 chrX:1279145-1279265 1.0000 120 chr3L:2575355-2575475 1.0000 120 chr3R:11869350-11869470 1.0000 120 chr2R:11074110-11074230 1.0000 120 chr2L:5044540-5044660 1.0000 120 chr3L:15589798-15589918 1.0000 120 chrX:17423439-17423559 1.0000 120 chr3R:23526212-23526332 1.0000 120 chr3R:16341511-16341631 1.0000 120 chrX:19146477-19146597 1.0000 120 chr3R:13051326-13051446 1.0000 120 chr3R:18988171-18988291 1.0000 120 chr2R:23042997-23043117 1.0000 120 chr2R:12870715-12870835 1.0000 120 chr2R:11712213-11712333 1.0000 120 chr3R:26867640-26867760 1.0000 120 chr2R:22911894-22912014 1.0000 120 chr3R:26956523-26956643 1.0000 120 chr3L:15968501-15968621 1.0000 120 chr2R:22668047-22668167 1.0000 120 chr3R:21446503-21446623 1.0000 120 chr3L:7862495-7862615 1.0000 120 chr2R:20831887-20832007 1.0000 120 chrX:3538926-3539046 1.0000 120 chr3L:17962478-17962598 1.0000 120 chr3L:1298698-1298818 1.0000 120 chr3R:29841638-29841758 1.0000 120 chrX:18533377-18533497 1.0000 120 chrX:9588001-9588121 1.0000 120 chr3R:5218226-5218346 1.0000 120 chr2R:13429776-13429896 1.0000 120 chr2L:15910001-15910121 1.0000 120 chr2L:16881174-16881294 1.0000 120 chr2R:18799720-18799840 1.0000 120 chr3L:11358816-11358936 1.0000 120 chrX:11683604-11683724 1.0000 120 chr3R:31709250-31709370 1.0000 120 chr3R:23736462-23736582 1.0000 120 chr3R:6816272-6816392 1.0000 120 chrX:9120031-9120151 1.0000 120 chr3R:9436799-9436919 1.0000 120 chr2R:22998764-22998884 1.0000 120 chr2L:20796958-20797078 1.0000 120 chr2L:5887009-5887129 1.0000 120 chr2R:12983615-12983735 1.0000 120 chr3R:16847298-16847418 1.0000 120 chr3L:9762231-9762351 1.0000 120 chr3L:16646918-16647038 1.0000 120 chr3R:25515484-25515604 1.0000 120 chr2R:17870206-17870326 1.0000 120 chr3R:16223379-16223499 1.0000 120 chr3L:753868-753988 1.0000 120 chr3R:16948733-16948853 1.0000 120 chr2R:24581246-24581366 1.0000 120 chrX:16781249-16781369 1.0000 120 chr2R:6649232-6649352 1.0000 120 chr3L:6807643-6807763 1.0000 120 chr3L:12178918-12179038 1.0000 120 chr3L:15967170-15967290 1.0000 120 chr3L:12507570-12507690 1.0000 120 chr2R:23203658-23203778 1.0000 120 chr3R:4962748-4962868 1.0000 120 chr3L:629837-629957 1.0000 120 chr3R:14098634-14098754 1.0000 120 chr3R:14391076-14391196 1.0000 120 chr3R:22041737-22041857 1.0000 120 chr2R:14001874-14001994 1.0000 120 chr3L:1674404-1674524 1.0000 120 chr3L:4101773-4101893 1.0000 120 chrX:8112862-8112982 1.0000 120 chrX:19168113-19168233 1.0000 120 chrX:10744486-10744606 1.0000 120 chr2R:6938588-6938708 1.0000 120 chr2R:18628228-18628348 1.0000 120 chrX:19763596-19763716 1.0000 120 chr2R:22545981-22546101 1.0000 120 chr3L:15125317-15125437 1.0000 120 chrX:948279-948399 1.0000 120 chrX:19276418-19276538 1.0000 120 chr3L:9854985-9855105 1.0000 120 chr2R:12200477-12200597 1.0000 120 chr2R:23203865-23203985 1.0000 120 chr3R:4684985-4685105 1.0000 120 chr3L:6904119-6904239 1.0000 120 chr2R:9494431-9494551 1.0000 120 chr2R:22450449-22450569 1.0000 120 chr2L:9907425-9907545 1.0000 120 chr3R:10605219-10605339 1.0000 120 chr3R:21875207-21875327 1.0000 120 chr3R:23963037-23963157 1.0000 120 chr2L:10321232-10321352 1.0000 120 chr3R:20558282-20558402 1.0000 120 chr2R:11528126-11528246 1.0000 120 chr3R:13382992-13383112 1.0000 120 chrX:5690918-5691038 1.0000 120 chr3R:26980535-26980655 1.0000 120 chr3R:26799010-26799130 1.0000 120 chr3R:6724094-6724214 1.0000 120 chrX:5560637-5560757 1.0000 120 chrX:15333370-15333490 1.0000 120 chr2R:20552076-20552196 1.0000 120 chr3L:11419557-11419677 1.0000 120 chr2R:21091933-21092053 1.0000 120 chr3L:11286628-11286748 1.0000 120 chr2R:6494351-6494471 1.0000 120 chr2L:1650106-1650226 1.0000 120 chrX:16650515-16650635 1.0000 120 chrX:3950278-3950398 1.0000 120 chr3R:4360731-4360851 1.0000 120 chr3L:13845419-13845539 1.0000 120 chr2L:11130904-11131024 1.0000 120 chr3L:8853067-8853187 1.0000 120 chrX:5889100-5889220 1.0000 120 chr3R:29068917-29069037 1.0000 120 chr3R:16158094-16158214 1.0000 120 chr2R:24275664-24275784 1.0000 120 chr3L:20389102-20389222 1.0000 120 chr3R:9872267-9872387 1.0000 120 chr2L:17260710-17260830 1.0000 120 chr2L:14021829-14021949 1.0000 120 chr3R:16225896-16226016 1.0000 120 chr2L:16816102-16816222 1.0000 120 chr3R:31086468-31086588 1.0000 120 chr2R:7636721-7636841 1.0000 120 chr3L:5182465-5182585 1.0000 120 chrX:17830232-17830352 1.0000 120 chr3R:29725652-29725772 1.0000 120 chrX:17176689-17176809 1.0000 120 chr3R:29088351-29088471 1.0000 120 chrX:11146944-11147064 1.0000 120 chrX:18512331-18512451 1.0000 120 chr3L:22136061-22136181 1.0000 120 chr2R:9929532-9929652 1.0000 120 chr3L:7634939-7635059 1.0000 120 chr2L:20078907-20079027 1.0000 120 chr3R:29699317-29699437 1.0000 120 chrX:17768377-17768497 1.0000 120 chr2R:14008405-14008525 1.0000 120 chr3R:23942858-23942978 1.0000 120 chr3R:15920858-15920978 1.0000 120 chr3R:30563318-30563438 1.0000 120 chrX:7110265-7110385 1.0000 120 chr2R:8327279-8327399 1.0000 120 chr3R:10024188-10024308 1.0000 120 chr3L:12804991-12805111 1.0000 120 chrX:6663280-6663400 1.0000 120 chr2R:24571644-24571764 1.0000 120 chr2R:17458938-17459058 1.0000 120 chr3R:19096934-19097054 1.0000 120 chr2L:4403166-4403286 1.0000 120 chr3R:14356732-14356852 1.0000 120 chr2L:9449031-9449151 1.0000 120 chr3L:6752333-6752453 1.0000 120 chr3L:19132740-19132860 1.0000 120 chr2L:18320092-18320212 1.0000 120 chr3R:6678616-6678736 1.0000 120 chr2R:22561984-22562104 1.0000 120 chr2R:9543669-9543789 1.0000 120 chr3L:378157-378277 1.0000 120 chr3L:9509280-9509400 1.0000 120 chr3L:16806507-16806627 1.0000 120 chr2R:21659877-21659997 1.0000 120 chr2R:20111258-20111378 1.0000 120 chr2R:15613852-15613972 1.0000 120 chr3R:25652204-25652324 1.0000 120 chr2L:12586995-12587115 1.0000 120 chr3L:8440982-8441102 1.0000 120 chr2R:24305999-24306119 1.0000 120 chr2L:20066472-20066592 1.0000 120 chr3L:21011126-21011246 1.0000 120 chr2L:20148552-20148672 1.0000 120 chr2R:9548186-9548306 1.0000 120 chr3R:25215219-25215339 1.0000 120 chr3R:11993226-11993346 1.0000 120 chrX:18517657-18517777 1.0000 120 chr3R:8784921-8785041 1.0000 120 chr3R:11157127-11157247 1.0000 120 chr3R:31311118-31311238 1.0000 120 chr3R:21850236-21850356 1.0000 120 chr3R:18315391-18315511 1.0000 120 chrX:618802-618922 1.0000 120 chr3L:16760410-16760530 1.0000 120 chrX:5517308-5517428 1.0000 120 chrX:3779891-3780011 1.0000 120 chr2L:22024587-22024707 1.0000 120 chr3L:11708252-11708372 1.0000 120 chr2R:19291987-19292107 1.0000 120 chr2R:9414334-9414454 1.0000 120 chrX:18239460-18239580 1.0000 120 chr3R:9157934-9158054 1.0000 120 chrX:6279173-6279293 1.0000 120 chr2L:9634219-9634339 1.0000 120 chrX:12221712-12221832 1.0000 120 chr3L:17949191-17949311 1.0000 120 chr2L:13878922-13879042 1.0000 120 chr2R:18536731-18536851 1.0000 120 chr3R:31669384-31669504 1.0000 120 chr3R:22447405-22447525 1.0000 120 chr2L:6179165-6179285 1.0000 120 chr2R:18539948-18540068 1.0000 120 chr2L:6956902-6957022 1.0000 120 chrX:1349379-1349499 1.0000 120 chr2L:7940831-7940951 1.0000 120 chr3L:22407729-22407849 1.0000 120 chrX:7703110-7703230 1.0000 120 chr3R:9055200-9055320 1.0000 120 chrX:16683898-16684018 1.0000 120 chr2R:11469679-11469799 1.0000 120 chr3R:10203700-10203820 1.0000 120 chr2L:22019034-22019154 1.0000 120 chr3R:25027766-25027886 1.0000 120 chr3R:16655595-16655715 1.0000 120 chr3R:32068158-32068278 1.0000 120 chrX:6220055-6220175 1.0000 120 chr2L:10967353-10967473 1.0000 120 chr2R:12025161-12025281 1.0000 120 chr3R:22664419-22664539 1.0000 120 chr3L:14672740-14672860 1.0000 120 chr3R:12408322-12408442 1.0000 120 chr2L:15762612-15762732 1.0000 120 chr3R:4714154-4714274 1.0000 120 chr3R:5300730-5300850 1.0000 120 chr2R:22270856-22270976 1.0000 120 chrX:5312210-5312330 1.0000 120 chr2R:13337209-13337329 1.0000 120 chr3R:27245313-27245433 1.0000 120 chr2R:23746605-23746725 1.0000 120 chrX:6109995-6110115 1.0000 120 chr2R:9388578-9388698 1.0000 120 chr2R:7381600-7381720 1.0000 120 chrX:10738979-10739099 1.0000 120 chrX:13332910-13333030 1.0000 120 chr3R:23922345-23922465 1.0000 120 chr2R:12274329-12274449 1.0000 120 chr2L:20822947-20823067 1.0000 120 chr2R:14913201-14913321 1.0000 120 chr3R:29089761-29089881 1.0000 120 chr3R:4996728-4996848 1.0000 120 chr2R:8018926-8019046 1.0000 120 chr2R:8649520-8649640 1.0000 120 chrX:16967588-16967708 1.0000 120 chr3L:21276959-21277079 1.0000 120 chrX:2340191-2340311 1.0000 120 chr2R:12705191-12705311 1.0000 120 chr3R:10140400-10140520 1.0000 120 chr3L:18114495-18114615 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_pb/ -dna -nmotifs 5 -w 8 -maxsize 250000 -nostatus ../result/final_prediction/fly/fasta/RankLinear8.0_60/pb.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 0.254 C 0.242 G 0.249 T 0.254 Background letter frequencies (from file dataset with add-one prior applied): A 0.254 C 0.242 G 0.249 T 0.254 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF TYTCGCTC MEME-1 width = 8 sites = 28 llr = 257 E-value = 5.9e-002 ******************************************************************************** -------------------------------------------------------------------------------- Motif TYTCGCTC MEME-1 Description -------------------------------------------------------------------------------- Simplified A ::::2::: pos.-specific C :6:a:a:a probability G 11::7::: matrix T 93a:1:a: bits 2.0 ** *** 1.8 ** *** 1.6 * ** *** 1.4 * ** *** Relative 1.2 * ** *** Entropy 1.0 * ** *** (13.2 bits) 0.8 * ****** 0.6 ******** 0.4 ******** 0.2 ******** 0.0 -------- Multilevel TCTCGCTC consensus T sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TYTCGCTC MEME-1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr2R:9548186-9548306 82 1.40e-05 tctctctctc tctcgctc tttttctctc chr3L:378157-378277 12 1.40e-05 CGTAACGCCA TCTCGCTC ACACACACGC chr3R:6678616-6678736 90 1.40e-05 GCGACTGCCG TCTCGCTC GCTCCCTGGG chr2R:8327279-8327399 30 1.40e-05 CCGGTCGCTT TCTCGCTC GCACCCGCTG chr2R:14008405-14008525 47 1.40e-05 CCAGTTGCCT TCTCGCTC CCCCAGCCAC chrX:17768377-17768497 29 1.40e-05 ATCTACCCGc tctcgctc gctctctctc chrX:15333370-15333490 25 1.40e-05 cgtctctctc tctcgctc CGCCTCGCAA chr2R:11528126-11528246 83 1.40e-05 gctcgctccc tctcgctc tcactctctc chr3L:6904119-6904239 55 1.40e-05 TTTAGTGTCA TCTCGCTC TGGCCATCGC chr3R:16847298-16847418 44 1.40e-05 CCACTCGCCG TCTCGCTC CCACCAAAAT chr3R:21446503-21446623 35 1.40e-05 GGTAGTGTCA TCTCGCTC TGCTCGGCTC chr3L:9509280-9509400 76 2.87e-05 CGCACCGGTA TTTCGCTC AGTTCGGAGA chr3R:10024188-10024308 113 2.87e-05 ATCGGTATTT TTTCGCTC chr3L:15967170-15967290 26 2.87e-05 TATATCCTTC TTTCGCTC CCGATCCTTT chr2R:20831887-20832007 33 2.87e-05 GGCACCTCTC TTTCGCTC GCTTTGTGTA chr3L:7862495-7862615 13 4.30e-05 TATATTTCCT TCTCACTC TGTATTTATT chr2L:18320092-18320212 52 5.74e-05 AGTCGTTCTC TGTCGCTC TTGGATTGCG chr3L:8853067-8853187 111 5.74e-05 AGGTGGGCCC TGTCGCTC AG chr3L:1674404-1674524 24 5.74e-05 ATTAGCCATA TGTCGCTC GCATTCAGAT chr2R:15613852-15613972 54 7.16e-05 TTCTCCTGCC TCTCTCTC TTGCCCAGCC chr3R:21875207-21875327 20 7.16e-05 TATATAGCCT TCTCTCTC GCTTCTTAGC chr2R:13337209-13337329 69 8.66e-05 AAATACCccg tttcactc cgaaccgctc chr3R:9055200-9055320 73 8.66e-05 AACTAGTGAA TTTCACTC AAACGTGGCG chrX:3779891-3780011 3 8.66e-05 CT TTTCACTC CCCACGGTGT chr2L:20796958-20797078 26 8.66e-05 CGGCTAAGAA TTTCACTC CTCCAACAGC chr2R:23203658-23203778 72 1.02e-04 CTACCCTGTT TTTCTCTC ACGAAGTTGC chr2R:20111258-20111378 82 1.15e-04 ATGTGTGTGT GCTCGCTC GTGAGAGTGC chr3R:9436799-9436919 63 1.15e-04 cgtttcgtgc gctcgctc gatcgctcgc -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TYTCGCTC MEME-1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr2R:9548186-9548306 1.4e-05 81_[+1]_31 chr3L:378157-378277 1.4e-05 11_[+1]_101 chr3R:6678616-6678736 1.4e-05 89_[+1]_23 chr2R:8327279-8327399 1.4e-05 29_[+1]_83 chr2R:14008405-14008525 1.4e-05 46_[+1]_66 chrX:17768377-17768497 1.4e-05 28_[+1]_84 chrX:15333370-15333490 1.4e-05 24_[+1]_88 chr2R:11528126-11528246 1.4e-05 82_[+1]_30 chr3L:6904119-6904239 1.4e-05 54_[+1]_58 chr3R:16847298-16847418 1.4e-05 43_[+1]_69 chr3R:21446503-21446623 1.4e-05 34_[+1]_78 chr3L:9509280-9509400 2.9e-05 75_[+1]_37 chr3R:10024188-10024308 2.9e-05 112_[+1] chr3L:15967170-15967290 2.9e-05 25_[+1]_87 chr2R:20831887-20832007 2.9e-05 32_[+1]_80 chr3L:7862495-7862615 4.3e-05 12_[+1]_100 chr2L:18320092-18320212 5.7e-05 51_[+1]_61 chr3L:8853067-8853187 5.7e-05 110_[+1]_2 chr3L:1674404-1674524 5.7e-05 23_[+1]_89 chr2R:15613852-15613972 7.2e-05 53_[+1]_59 chr3R:21875207-21875327 7.2e-05 19_[+1]_93 chr2R:13337209-13337329 8.7e-05 68_[+1]_44 chr3R:9055200-9055320 8.7e-05 72_[+1]_40 chrX:3779891-3780011 8.7e-05 2_[+1]_110 chr2L:20796958-20797078 8.7e-05 25_[+1]_87 chr2R:23203658-23203778 0.0001 71_[+1]_41 chr2R:20111258-20111378 0.00012 81_[+1]_31 chr3R:9436799-9436919 0.00012 62_[+1]_50 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TYTCGCTC MEME-1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF TYTCGCTC width=8 seqs=28 chr2R:9548186-9548306 ( 82) TCTCGCTC 1 chr3L:378157-378277 ( 12) TCTCGCTC 1 chr3R:6678616-6678736 ( 90) TCTCGCTC 1 chr2R:8327279-8327399 ( 30) TCTCGCTC 1 chr2R:14008405-14008525 ( 47) TCTCGCTC 1 chrX:17768377-17768497 ( 29) TCTCGCTC 1 chrX:15333370-15333490 ( 25) TCTCGCTC 1 chr2R:11528126-11528246 ( 83) TCTCGCTC 1 chr3L:6904119-6904239 ( 55) TCTCGCTC 1 chr3R:16847298-16847418 ( 44) TCTCGCTC 1 chr3R:21446503-21446623 ( 35) TCTCGCTC 1 chr3L:9509280-9509400 ( 76) TTTCGCTC 1 chr3R:10024188-10024308 ( 113) TTTCGCTC 1 chr3L:15967170-15967290 ( 26) TTTCGCTC 1 chr2R:20831887-20832007 ( 33) TTTCGCTC 1 chr3L:7862495-7862615 ( 13) TCTCACTC 1 chr2L:18320092-18320212 ( 52) TGTCGCTC 1 chr3L:8853067-8853187 ( 111) TGTCGCTC 1 chr3L:1674404-1674524 ( 24) TGTCGCTC 1 chr2R:15613852-15613972 ( 54) TCTCTCTC 1 chr3R:21875207-21875327 ( 20) TCTCTCTC 1 chr2R:13337209-13337329 ( 69) TTTCACTC 1 chr3R:9055200-9055320 ( 73) TTTCACTC 1 chrX:3779891-3780011 ( 3) TTTCACTC 1 chr2L:20796958-20797078 ( 26) TTTCACTC 1 chr2R:23203658-23203778 ( 72) TTTCTCTC 1 chr2R:20111258-20111378 ( 82) GCTCGCTC 1 chr3R:9436799-9436919 ( 63) GCTCGCTC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TYTCGCTC MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 28250 bayes= 11.2004 E= 5.9e-002 -1145 -1145 -180 187 -1145 124 -122 34 -1145 -1145 -1145 197 -1145 205 -1145 -1145 -51 -1145 152 -125 -1145 205 -1145 -1145 -1145 -1145 -1145 197 -1145 205 -1145 -1145 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TYTCGCTC MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 28 E= 5.9e-002 0.000000 0.000000 0.071429 0.928571 0.000000 0.571429 0.107143 0.321429 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.178571 0.000000 0.714286 0.107143 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TYTCGCTC MEME-1 regular expression -------------------------------------------------------------------------------- T[CT]TCGCTC -------------------------------------------------------------------------------- Time 8.31 secs. ******************************************************************************** ******************************************************************************** MOTIF GCGCTGCG MEME-2 width = 8 sites = 9 llr = 96 E-value = 2.2e+004 ******************************************************************************** -------------------------------------------------------------------------------- Motif GCGCTGCG MEME-2 Description -------------------------------------------------------------------------------- Simplified A ::::2::: pos.-specific C :a:a::a: probability G a:a::a:a matrix T ::::8::: bits 2.0 **** *** 1.8 **** *** 1.6 **** *** 1.4 **** *** Relative 1.2 ******** Entropy 1.0 ******** (15.4 bits) 0.8 ******** 0.6 ******** 0.4 ******** 0.2 ******** 0.0 -------- Multilevel GCGCTGCG consensus A sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCGCTGCG MEME-2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chrX:6220055-6220175 99 1.38e-05 GGTGAAGGTC GCGCTGCG AAAGAGCGAG chr2R:9414334-9414454 107 1.38e-05 TTTCGTGGCG GCGCTGCG CATGCG chr3L:378157-378277 42 1.38e-05 GTAGCCCATT GCGCTGCG TTTATATACT chr3R:15920858-15920978 24 1.38e-05 GATAGCCTCT GCGCTGCG ACTCGCACTC chr2R:9929532-9929652 55 1.38e-05 TGAAGAAGCG GCGCTGCG GACGCGTACA chr3R:23963037-23963157 98 1.38e-05 AGCGATAAAG GCGCTGCG CCGCGAGAAA chr3R:16847298-16847418 26 1.38e-05 GTCGACGCCT GCGCTGCG CCACTCGCCG chr2R:20111258-20111378 54 2.77e-05 agcgaaagca gcgcagcg acagcgTGGC chr3R:29088351-29088471 24 2.77e-05 GACGCGAAGA GCGCAGCG TGGCAGCGTA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCGCTGCG MEME-2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrX:6220055-6220175 1.4e-05 98_[+2]_14 chr2R:9414334-9414454 1.4e-05 106_[+2]_6 chr3L:378157-378277 1.4e-05 41_[+2]_71 chr3R:15920858-15920978 1.4e-05 23_[+2]_89 chr2R:9929532-9929652 1.4e-05 54_[+2]_58 chr3R:23963037-23963157 1.4e-05 97_[+2]_15 chr3R:16847298-16847418 1.4e-05 25_[+2]_87 chr2R:20111258-20111378 2.8e-05 53_[+2]_59 chr3R:29088351-29088471 2.8e-05 23_[+2]_89 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCGCTGCG MEME-2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF GCGCTGCG width=8 seqs=9 chrX:6220055-6220175 ( 99) GCGCTGCG 1 chr2R:9414334-9414454 ( 107) GCGCTGCG 1 chr3L:378157-378277 ( 42) GCGCTGCG 1 chr3R:15920858-15920978 ( 24) GCGCTGCG 1 chr2R:9929532-9929652 ( 55) GCGCTGCG 1 chr3R:23963037-23963157 ( 98) GCGCTGCG 1 chr3R:16847298-16847418 ( 26) GCGCTGCG 1 chr2R:20111258-20111378 ( 54) GCGCAGCG 1 chr3R:29088351-29088471 ( 24) GCGCAGCG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCGCTGCG MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 28250 bayes= 11.7499 E= 2.2e+004 -982 -982 200 -982 -982 205 -982 -982 -982 -982 200 -982 -982 205 -982 -982 -19 -982 -982 161 -982 -982 200 -982 -982 205 -982 -982 -982 -982 200 -982 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCGCTGCG MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 9 E= 2.2e+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 0.222222 0.000000 0.000000 0.777778 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 GCGCTGCG MEME-2 regular expression -------------------------------------------------------------------------------- GCGC[TA]GCG -------------------------------------------------------------------------------- Time 14.55 secs. ******************************************************************************** ******************************************************************************** MOTIF AGCGAGAG MEME-3 width = 8 sites = 18 llr = 170 E-value = 2.8e+004 ******************************************************************************** -------------------------------------------------------------------------------- Motif AGCGAGAG MEME-3 Description -------------------------------------------------------------------------------- Simplified A a:1:819: pos.-specific C ::8:::1: probability G :a:a29:a matrix T ::1::::: bits 2.0 ** * * 1.8 ** * * 1.6 ** * ** 1.4 ** * *** Relative 1.2 ******** Entropy 1.0 ******** (13.6 bits) 0.8 ******** 0.6 ******** 0.4 ******** 0.2 ******** 0.0 -------- Multilevel AGCGAGAG consensus G sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AGCGAGAG MEME-3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chrX:6220055-6220175 69 1.52e-05 CCCATAGGCG AGCGAGAG AGATAGAAAA chr2L:22019034-22019154 46 1.52e-05 GGTAAGCGTA AGCGAGAG CCGCCGCTAT chr3L:17949191-17949311 24 1.52e-05 GGGTAGTGCG AGCGAGAG GGGCCGGGAA chr2L:9634219-9634339 53 1.52e-05 CGGAAACGAA AGCGAGAG AGAGAAAGAA chr3L:21011126-21011246 23 1.52e-05 CGAAGGAGCG AGCGAGAG GGACGCTGAG chr3L:9509280-9509400 3 1.52e-05 GA AGCGAGAG GGGTGATGGG chr3R:23963037-23963157 10 1.52e-05 TCAGCGTCG AGCGAGAG GGCGCGATTG chr3R:16948733-16948853 31 1.52e-05 GTCAAGTGAG AGCGAGAG GCAAGAGTAA chr3L:16806507-16806627 49 3.02e-05 ATGCGGAGCG AGCGGGAG AGCAGAGCAG chr3R:4360731-4360851 16 3.02e-05 CCCAACAGCA AGCGGGAG TAAGGGTGCT chr2R:14001874-14001994 40 3.02e-05 GAAAATGCAG AGCGGGAG GGCGATATGA chrX:11683604-11683724 77 3.02e-05 CGGAATCGGC AGCGGGAG GCGCCCAACG chr2L:10967353-10967473 52 4.62e-05 CAATAATGAG AGTGAGAG TGCGGAGAAG chr2R:8327279-8327399 7 4.62e-05 gcagtg agtgagag agaCCCCGGT chr3R:32068158-32068278 14 6.17e-05 ACACTCTCCC AGCGAAAG AGAGACACAG chr2R:20111258-20111378 44 6.17e-05 cagagcagag agcgaaag cagcgcagcg chrX:10738979-10739099 8 9.23e-05 GAGAGGG AGAGAGAG CGCGAGCGGC chr3L:22136061-22136181 51 9.23e-05 GAAGTTTCCC AGCGAGCG GTACACGGGC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AGCGAGAG MEME-3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrX:6220055-6220175 1.5e-05 68_[+3]_44 chr2L:22019034-22019154 1.5e-05 45_[+3]_67 chr3L:17949191-17949311 1.5e-05 23_[+3]_89 chr2L:9634219-9634339 1.5e-05 52_[+3]_60 chr3L:21011126-21011246 1.5e-05 22_[+3]_90 chr3L:9509280-9509400 1.5e-05 2_[+3]_110 chr3R:23963037-23963157 1.5e-05 9_[+3]_103 chr3R:16948733-16948853 1.5e-05 30_[+3]_82 chr3L:16806507-16806627 3e-05 48_[+3]_64 chr3R:4360731-4360851 3e-05 15_[+3]_97 chr2R:14001874-14001994 3e-05 39_[+3]_73 chrX:11683604-11683724 3e-05 76_[+3]_36 chr2L:10967353-10967473 4.6e-05 51_[+3]_61 chr2R:8327279-8327399 4.6e-05 6_[+3]_106 chr3R:32068158-32068278 6.2e-05 13_[+3]_99 chr2R:20111258-20111378 6.2e-05 43_[+3]_69 chrX:10738979-10739099 9.2e-05 7_[+3]_105 chr3L:22136061-22136181 9.2e-05 50_[+3]_62 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AGCGAGAG MEME-3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF AGCGAGAG width=8 seqs=18 chrX:6220055-6220175 ( 69) AGCGAGAG 1 chr2L:22019034-22019154 ( 46) AGCGAGAG 1 chr3L:17949191-17949311 ( 24) AGCGAGAG 1 chr2L:9634219-9634339 ( 53) AGCGAGAG 1 chr3L:21011126-21011246 ( 23) AGCGAGAG 1 chr3L:9509280-9509400 ( 3) AGCGAGAG 1 chr3R:23963037-23963157 ( 10) AGCGAGAG 1 chr3R:16948733-16948853 ( 31) AGCGAGAG 1 chr3L:16806507-16806627 ( 49) AGCGGGAG 1 chr3R:4360731-4360851 ( 16) AGCGGGAG 1 chr2R:14001874-14001994 ( 40) AGCGGGAG 1 chrX:11683604-11683724 ( 77) AGCGGGAG 1 chr2L:10967353-10967473 ( 52) AGTGAGAG 1 chr2R:8327279-8327399 ( 7) AGTGAGAG 1 chr3R:32068158-32068278 ( 14) AGCGAAAG 1 chr2R:20111258-20111378 ( 44) AGCGAAAG 1 chrX:10738979-10739099 ( 8) AGAGAGAG 1 chr3L:22136061-22136181 ( 51) AGCGAGCG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AGCGAGAG MEME-3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 28250 bayes= 11.4635 E= 2.8e+004 198 -1081 -1081 -1081 -1081 -1081 200 -1081 -219 178 -1081 -119 -1081 -1081 200 -1081 161 -1081 -17 -1081 -119 -1081 183 -1081 189 -212 -1081 -1081 -1081 -1081 200 -1081 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AGCGAGAG MEME-3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 18 E= 2.8e+004 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.055556 0.833333 0.000000 0.111111 0.000000 0.000000 1.000000 0.000000 0.777778 0.000000 0.222222 0.000000 0.111111 0.000000 0.888889 0.000000 0.944444 0.055556 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AGCGAGAG MEME-3 regular expression -------------------------------------------------------------------------------- AGCG[AG]GAG -------------------------------------------------------------------------------- Time 20.79 secs. ******************************************************************************** ******************************************************************************** MOTIF CCGCYGCC MEME-4 width = 8 sites = 14 llr = 134 E-value = 4.2e+005 ******************************************************************************** -------------------------------------------------------------------------------- Motif CCGCYGCC MEME-4 Description -------------------------------------------------------------------------------- Simplified A :31::::: pos.-specific C a7:a6:aa probability G ::9::a:: matrix T ::::4::: bits 2.0 * * *** 1.8 * * *** 1.6 * * *** 1.4 * ** *** Relative 1.2 **** *** Entropy 1.0 ******** (13.8 bits) 0.8 ******** 0.6 ******** 0.4 ******** 0.2 ******** 0.0 -------- Multilevel CCGCCGCC consensus A T sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCGCYGCC MEME-4 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr2R:18539948-18540068 37 1.25e-05 GCTCGAGCAG CCGCCGCC GCAGCTTCGA chrX:18512331-18512451 81 1.25e-05 aacgccaccg ccgccgcc gcAAGCGCGA chr2L:11130904-11131024 84 1.25e-05 gcagccgccg ccgccgcc gccACTGCAA chr3R:10605219-10605339 5 1.25e-05 GCCG CCGCCGCC GCTGCGTGCG chr2R:20831887-20832007 101 1.25e-05 CTCTGTCGCT CCGCCGCC GTCGCTGTTG chr2R:6494351-6494471 44 2.55e-05 CTACAACCGA CCGCTGCC GGCTGCGAAG chr3L:16646918-16647038 5 2.55e-05 CGAT CCGCTGCC ACTGGCCACG chr3R:26867640-26867760 111 2.55e-05 GCCGTGTACT CCGCTGCC AT chr3R:16158094-16158214 87 3.86e-05 AACGCCGCAA CAGCCGCC CTTTGCCGTC chr2R:12870715-12870835 85 3.86e-05 GCCGGCTCTT CAGCCGCC GATGCCGGTG chr3R:9872267-9872387 94 5.23e-05 TCAAGTGCAA CAGCTGCC AAGAACTTTT chr3L:753868-753988 80 5.23e-05 GCGCTACCCG CAGCTGCC Tgcccaccca chr3R:16341511-16341631 4 6.50e-05 GGA CCACCGCC CCGCGGGAAC chr2L:15249208-15249328 10 6.50e-05 CTCCCGTCT CCACCGCC TCGTCGGCTG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCGCYGCC MEME-4 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr2R:18539948-18540068 1.2e-05 36_[+4]_76 chrX:18512331-18512451 1.2e-05 80_[+4]_32 chr2L:11130904-11131024 1.2e-05 83_[+4]_29 chr3R:10605219-10605339 1.2e-05 4_[+4]_108 chr2R:20831887-20832007 1.2e-05 100_[+4]_12 chr2R:6494351-6494471 2.6e-05 43_[+4]_69 chr3L:16646918-16647038 2.6e-05 4_[+4]_108 chr3R:26867640-26867760 2.6e-05 110_[+4]_2 chr3R:16158094-16158214 3.9e-05 86_[+4]_26 chr2R:12870715-12870835 3.9e-05 84_[+4]_28 chr3R:9872267-9872387 5.2e-05 93_[+4]_19 chr3L:753868-753988 5.2e-05 79_[+4]_33 chr3R:16341511-16341631 6.5e-05 3_[+4]_109 chr2L:15249208-15249328 6.5e-05 9_[+4]_103 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCGCYGCC MEME-4 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF CCGCYGCC width=8 seqs=14 chr2R:18539948-18540068 ( 37) CCGCCGCC 1 chrX:18512331-18512451 ( 81) CCGCCGCC 1 chr2L:11130904-11131024 ( 84) CCGCCGCC 1 chr3R:10605219-10605339 ( 5) CCGCCGCC 1 chr2R:20831887-20832007 ( 101) CCGCCGCC 1 chr2R:6494351-6494471 ( 44) CCGCTGCC 1 chr3L:16646918-16647038 ( 5) CCGCTGCC 1 chr3R:26867640-26867760 ( 111) CCGCTGCC 1 chr3R:16158094-16158214 ( 87) CAGCCGCC 1 chr2R:12870715-12870835 ( 85) CAGCCGCC 1 chr3R:9872267-9872387 ( 94) CAGCTGCC 1 chr3L:753868-753988 ( 80) CAGCTGCC 1 chr3R:16341511-16341631 ( 4) CCACCGCC 1 chr2L:15249208-15249328 ( 10) CCACCGCC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCGCYGCC MEME-4 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 28250 bayes= 12.6482 E= 4.2e+005 -1045 205 -1045 -1045 17 156 -1045 -1045 -83 -1045 178 -1045 -1045 205 -1045 -1045 -1045 141 -1045 49 -1045 -1045 200 -1045 -1045 205 -1045 -1045 -1045 205 -1045 -1045 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCGCYGCC MEME-4 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 14 E= 4.2e+005 0.000000 1.000000 0.000000 0.000000 0.285714 0.714286 0.000000 0.000000 0.142857 0.000000 0.857143 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.642857 0.000000 0.357143 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCGCYGCC MEME-4 regular expression -------------------------------------------------------------------------------- C[CA]GC[CT]GCC -------------------------------------------------------------------------------- Time 27.00 secs. ******************************************************************************** ******************************************************************************** MOTIF TKTTRTTK MEME-5 width = 8 sites = 27 llr = 242 E-value = 2.5e+003 ******************************************************************************** -------------------------------------------------------------------------------- Motif TKTTRTTK MEME-5 Description -------------------------------------------------------------------------------- Simplified A ::::4::: pos.-specific C :::::::: probability G :4::6::6 matrix T a6aa:aa4 bits 2.0 * ** ** 1.8 * ** ** 1.6 * ** ** 1.4 * ** ** Relative 1.2 * ** ** Entropy 1.0 ******** (12.9 bits) 0.8 ******** 0.6 ******** 0.4 ******** 0.2 ******** 0.0 -------- Multilevel TTTTGTTG consensus G A T sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TKTTRTTK MEME-5 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr3R:25215219-25215339 83 1.66e-05 GTCAAACATT TTTTGTTG TTTTTTTTAA chr2R:21659877-21659997 64 1.66e-05 ATTCTTCTGC TTTTGTTG CCGCAAAATG chr3R:21875207-21875327 100 1.66e-05 GTTATACGGC TTTTGTTG CCATCGGACG chr2L:20796958-20797078 97 1.66e-05 TGAAAACCGC TTTTGTTG CAGGTGATGC chr2R:13429776-13429896 93 1.66e-05 GGCACGACTT TTTTGTTG GCGGTTCGAA chrX:5312210-5312330 37 3.36e-05 TGGGCCGCCA TTTTGTTT AGCGGCCACG chr3L:8440982-8441102 38 3.36e-05 CTTGAATTGT TTTTGTTT TATTCGAGAG chr3L:378157-378277 104 3.36e-05 gagagCGTGC TTTTGTTT GGCGCTGCA chr2R:8327279-8327399 82 3.36e-05 CTCGCCTTCG TTTTGTTT GCTCGTGTtt chr3L:6904119-6904239 40 3.36e-05 ATAGCAGCCA TTTTGTTT AGTGTCATCT chr2R:12705191-12705311 76 5.00e-05 CGGCGTCGTT TGTTGTTG TTTGCGAATG chrX:17830232-17830352 32 5.00e-05 GCTGCTGCTT TGTTGTTG TTTGCCTTTC chr2L:14021829-14021949 63 5.00e-05 ATGTTGCTGT TGTTGTTG TCCCTGCGAC chr2L:9907425-9907545 90 5.00e-05 TAGTGCCTAT TGTTGTTG CTTTTGCTCG chr3L:4101773-4101893 104 5.00e-05 GGCGTTGCTT TGTTGTTG CTGCAATTT chr3L:1298698-1298818 60 5.00e-05 TGCTGCTACT TGTTGTTG CGCTGACGGC chr3R:13051326-13051446 68 6.69e-05 TTTTTCTTAC TTTTATTG GACATTGCTT chr3L:19349874-19349994 28 6.69e-05 AGGCTACGGT TTTTATTG CTCTTCCGGC chr3L:21276959-21277079 37 8.36e-05 GCTGGCTACA TGTTGTTT TTTGAGGCTC chr2R:11469679-11469799 17 1.01e-04 TTTATTAACC TTTTATTT AATGCTATTT chrX:6279173-6279293 44 1.01e-04 AAAAACTTGC TTTTATTT TACTTGCTCG chr3L:22136061-22136181 5 1.01e-04 CGTA TTTTATTT TACAGTCGAA chr3L:629837-629957 48 1.01e-04 TTTAAAAATG TTTTATTT CATTATTACG chr3L:753868-753988 19 1.01e-04 CCGCTTTTCC TTTTATTT CACGTACGAA chrX:3950278-3950398 16 1.18e-04 GTCATCGCAT TGTTATTG AACTCCTGTT chr2L:1650106-1650226 5 1.18e-04 GCAT TGTTATTG TTTTTGGCAA chrX:6663280-6663400 79 1.35e-04 AACCACAGAA TGTTATTT ATAAACCACG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TKTTRTTK MEME-5 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr3R:25215219-25215339 1.7e-05 82_[+5]_30 chr2R:21659877-21659997 1.7e-05 63_[+5]_49 chr3R:21875207-21875327 1.7e-05 99_[+5]_13 chr2L:20796958-20797078 1.7e-05 96_[+5]_16 chr2R:13429776-13429896 1.7e-05 92_[+5]_20 chrX:5312210-5312330 3.4e-05 36_[+5]_76 chr3L:8440982-8441102 3.4e-05 37_[+5]_75 chr3L:378157-378277 3.4e-05 103_[+5]_9 chr2R:8327279-8327399 3.4e-05 81_[+5]_31 chr3L:6904119-6904239 3.4e-05 39_[+5]_73 chr2R:12705191-12705311 5e-05 75_[+5]_37 chrX:17830232-17830352 5e-05 31_[+5]_81 chr2L:14021829-14021949 5e-05 62_[+5]_50 chr2L:9907425-9907545 5e-05 89_[+5]_23 chr3L:4101773-4101893 5e-05 103_[+5]_9 chr3L:1298698-1298818 5e-05 59_[+5]_53 chr3R:13051326-13051446 6.7e-05 67_[+5]_45 chr3L:19349874-19349994 6.7e-05 27_[+5]_85 chr3L:21276959-21277079 8.4e-05 36_[+5]_76 chr2R:11469679-11469799 0.0001 16_[+5]_96 chrX:6279173-6279293 0.0001 43_[+5]_69 chr3L:22136061-22136181 0.0001 4_[+5]_108 chr3L:629837-629957 0.0001 47_[+5]_65 chr3L:753868-753988 0.0001 18_[+5]_94 chrX:3950278-3950398 0.00012 15_[+5]_97 chr2L:1650106-1650226 0.00012 4_[+5]_108 chrX:6663280-6663400 0.00013 78_[+5]_34 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TKTTRTTK MEME-5 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF TKTTRTTK width=8 seqs=27 chr3R:25215219-25215339 ( 83) TTTTGTTG 1 chr2R:21659877-21659997 ( 64) TTTTGTTG 1 chr3R:21875207-21875327 ( 100) TTTTGTTG 1 chr2L:20796958-20797078 ( 97) TTTTGTTG 1 chr2R:13429776-13429896 ( 93) TTTTGTTG 1 chrX:5312210-5312330 ( 37) TTTTGTTT 1 chr3L:8440982-8441102 ( 38) TTTTGTTT 1 chr3L:378157-378277 ( 104) TTTTGTTT 1 chr2R:8327279-8327399 ( 82) TTTTGTTT 1 chr3L:6904119-6904239 ( 40) TTTTGTTT 1 chr2R:12705191-12705311 ( 76) TGTTGTTG 1 chrX:17830232-17830352 ( 32) TGTTGTTG 1 chr2L:14021829-14021949 ( 63) TGTTGTTG 1 chr2L:9907425-9907545 ( 90) TGTTGTTG 1 chr3L:4101773-4101893 ( 104) TGTTGTTG 1 chr3L:1298698-1298818 ( 60) TGTTGTTG 1 chr3R:13051326-13051446 ( 68) TTTTATTG 1 chr3L:19349874-19349994 ( 28) TTTTATTG 1 chr3L:21276959-21277079 ( 37) TGTTGTTT 1 chr2R:11469679-11469799 ( 17) TTTTATTT 1 chrX:6279173-6279293 ( 44) TTTTATTT 1 chr3L:22136061-22136181 ( 5) TTTTATTT 1 chr3L:629837-629957 ( 48) TTTTATTT 1 chr3L:753868-753988 ( 19) TTTTATTT 1 chrX:3950278-3950398 ( 16) TGTTATTG 1 chr2L:1650106-1650226 ( 5) TGTTATTG 1 chrX:6663280-6663400 ( 79) TGTTATTT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TKTTRTTK MEME-5 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 28250 bayes= 11.2246 E= 2.5e+003 -1140 -1140 -1140 197 -1140 -1140 57 131 -1140 -1140 -1140 197 -1140 -1140 -1140 197 54 -1140 134 -1140 -1140 -1140 -1140 197 -1140 -1140 -1140 197 -1140 -1140 116 80 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TKTTRTTK MEME-5 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 27 E= 2.5e+003 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.370370 0.629630 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.370370 0.000000 0.629630 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.555556 0.444444 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TKTTRTTK MEME-5 regular expression -------------------------------------------------------------------------------- T[TG]TT[GA]TT[GT] -------------------------------------------------------------------------------- Time 33.20 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr3L:11370016-11370136 8.39e-01 120 chr3L:19349874-19349994 9.35e-02 27_[+5(6.69e-05)]_85 chr2L:15249208-15249328 8.46e-02 9_[+4(6.50e-05)]_103 chrX:2036986-2037106 7.89e-01 120 chrX:1279145-1279265 7.91e-01 120 chr3L:2575355-2575475 9.02e-01 120 chr3R:11869350-11869470 3.76e-01 120 chr2R:11074110-11074230 6.60e-01 120 chr2L:5044540-5044660 4.78e-01 120 chr3L:15589798-15589918 9.00e-01 120 chrX:17423439-17423559 1.95e-01 120 chr3R:23526212-23526332 7.40e-01 120 chr3R:16341511-16341631 2.80e-02 3_[+4(6.50e-05)]_109 chrX:19146477-19146597 2.73e-01 49_[+5(5.00e-05)]_63 chr3R:13051326-13051446 1.75e-01 67_[+5(6.69e-05)]_45 chr3R:18988171-18988291 5.45e-01 120 chr2R:23042997-23043117 4.92e-01 120 chr2R:12870715-12870835 2.51e-02 84_[+4(3.86e-05)]_28 chr2R:11712213-11712333 3.83e-02 120 chr3R:26867640-26867760 1.43e-01 110_[+4(2.55e-05)]_2 chr2R:22911894-22912014 7.91e-01 120 chr3R:26956523-26956643 7.58e-01 120 chr3L:15968501-15968621 4.44e-01 120 chr2R:22668047-22668167 7.06e-01 120 chr3R:21446503-21446623 2.25e-02 34_[+1(1.40e-05)]_78 chr3L:7862495-7862615 8.31e-02 12_[+1(4.30e-05)]_100 chr2R:20831887-20832007 1.66e-03 32_[+1(2.87e-05)]_60_[+4(1.25e-05)]_\ 12 chrX:3538926-3539046 3.42e-01 120 chr3L:17962478-17962598 9.48e-01 120 chr3L:1298698-1298818 3.63e-02 59_[+5(5.00e-05)]_53 chr3R:29841638-29841758 8.33e-03 28_[+4(9.17e-05)]_84 chrX:18533377-18533497 9.84e-01 120 chrX:9588001-9588121 6.48e-01 120 chr3R:5218226-5218346 3.57e-01 120 chr2R:13429776-13429896 8.34e-03 92_[+5(1.66e-05)]_20 chr2L:15910001-15910121 4.11e-02 120 chr2L:16881174-16881294 5.04e-02 120 chr2R:18799720-18799840 9.47e-01 120 chr3L:11358816-11358936 5.94e-03 120 chrX:11683604-11683724 1.95e-03 30_[+2(5.44e-05)]_38_[+3(3.02e-05)]_\ 36 chr3R:31709250-31709370 7.83e-01 120 chr3R:23736462-23736582 9.85e-01 120 chr3R:6816272-6816392 1.44e-02 120 chrX:9120031-9120151 1.04e-01 120 chr3R:9436799-9436919 5.57e-02 120 chr2R:22998764-22998884 8.59e-02 120 chr2L:20796958-20797078 3.37e-04 25_[+1(8.66e-05)]_63_[+5(1.66e-05)]_\ 16 chr2L:5887009-5887129 3.72e-01 120 chr2R:12983615-12983735 7.01e-01 120 chr3R:16847298-16847418 7.23e-04 25_[+2(1.38e-05)]_10_[+1(1.40e-05)]_\ 26_[+1(2.87e-05)]_35 chr3L:9762231-9762351 6.34e-01 120 chr3L:16646918-16647038 1.06e-02 4_[+4(2.55e-05)]_108 chr3R:25515484-25515604 1.22e-01 120 chr2R:17870206-17870326 4.08e-01 120 chr3R:16223379-16223499 2.74e-01 120 chr3L:753868-753988 3.96e-03 79_[+4(5.23e-05)]_33 chr3R:16948733-16948853 2.51e-02 30_[+3(1.52e-05)]_82 chr2R:24581246-24581366 4.91e-01 120 chrX:16781249-16781369 6.69e-01 120 chr2R:6649232-6649352 3.24e-01 120 chr3L:6807643-6807763 9.31e-01 120 chr3L:12178918-12179038 8.21e-01 120 chr3L:15967170-15967290 9.58e-02 25_[+1(2.87e-05)]_87 chr3L:12507570-12507690 8.14e-01 120 chr2R:23203658-23203778 2.30e-01 120 chr3R:4962748-4962868 7.29e-01 120 chr3L:629837-629957 9.57e-02 120 chr3R:14098634-14098754 2.83e-01 120 chr3R:14391076-14391196 3.64e-01 120 chr3R:22041737-22041857 5.33e-01 120 chr2R:14001874-14001994 1.83e-01 39_[+3(3.02e-05)]_73 chr3L:1674404-1674524 4.75e-02 23_[+1(5.74e-05)]_89 chr3L:4101773-4101893 1.85e-01 103_[+5(5.00e-05)]_9 chrX:8112862-8112982 7.01e-01 120 chrX:19168113-19168233 7.51e-01 120 chrX:10744486-10744606 3.86e-01 120 chr2R:6938588-6938708 9.95e-01 120 chr2R:18628228-18628348 2.46e-01 120 chrX:19763596-19763716 3.10e-01 120 chr2R:22545981-22546101 4.14e-01 120 chr3L:15125317-15125437 5.59e-01 120 chrX:948279-948399 4.85e-01 120 chrX:19276418-19276538 5.40e-01 120 chr3L:9854985-9855105 2.39e-01 120 chr2R:12200477-12200597 1.83e-01 120 chr2R:23203865-23203985 1.70e-01 120 chr3R:4684985-4685105 9.03e-02 120 chr3L:6904119-6904239 5.54e-04 39_[+5(3.36e-05)]_7_[+1(1.40e-05)]_\ 26_[+1(1.40e-05)]_24 chr2R:9494431-9494551 6.90e-01 120 chr2R:22450449-22450569 4.57e-01 120 chr2L:9907425-9907545 3.35e-02 89_[+5(5.00e-05)]_23 chr3R:10605219-10605339 1.90e-02 1_[+4(1.25e-05)]_111 chr3R:21875207-21875327 3.40e-03 19_[+1(7.16e-05)]_72_[+5(1.66e-05)]_\ 13 chr3R:23963037-23963157 2.20e-03 9_[+3(1.52e-05)]_37_[+3(1.52e-05)]_\ 35_[+2(1.38e-05)]_15 chr2L:10321232-10321352 9.59e-01 120 chr3R:20558282-20558402 6.43e-02 120 chr2R:11528126-11528246 2.99e-02 68_[+1(1.40e-05)]_6_[+1(1.40e-05)]_\ 30 chr3R:13382992-13383112 6.73e-01 120 chrX:5690918-5691038 1.70e-01 120 chr3R:26980535-26980655 5.61e-01 120 chr3R:26799010-26799130 9.00e-02 120 chr3R:6724094-6724214 6.25e-01 120 chrX:5560637-5560757 1.44e-01 120 chrX:15333370-15333490 1.97e-02 16_[+1(7.16e-05)]_[+1(1.40e-05)]_88 chr2R:20552076-20552196 9.97e-01 120 chr3L:11419557-11419677 1.18e-01 120 chr2R:21091933-21092053 8.89e-01 120 chr3L:11286628-11286748 5.63e-01 120 chr2R:6494351-6494471 7.88e-02 43_[+4(2.55e-05)]_69 chr2L:1650106-1650226 4.72e-01 120 chrX:16650515-16650635 3.24e-01 120 chrX:3950278-3950398 2.98e-01 120 chr3R:4360731-4360851 1.61e-01 15_[+3(3.02e-05)]_97 chr3L:13845419-13845539 6.43e-01 120 chr2L:11130904-11131024 4.13e-03 77_[+4(1.25e-05)]_1_[+4(1.25e-05)]_\ 26 chr3L:8853067-8853187 8.77e-03 110_[+1(5.74e-05)]_2 chrX:5889100-5889220 9.28e-01 120 chr3R:29068917-29069037 9.43e-01 120 chr3R:16158094-16158214 9.82e-02 86_[+4(3.86e-05)]_26 chr2R:24275664-24275784 3.24e-01 120 chr3L:20389102-20389222 9.97e-01 120 chr3R:9872267-9872387 3.93e-02 93_[+4(5.23e-05)]_19 chr2L:17260710-17260830 4.39e-01 120 chr2L:14021829-14021949 1.73e-01 59_[+5(5.00e-05)]_53 chr3R:16225896-16226016 2.06e-01 58_[+2(5.44e-05)]_54 chr2L:16816102-16816222 3.52e-01 120 chr3R:31086468-31086588 5.00e-01 120 chr2R:7636721-7636841 7.31e-01 120 chr3L:5182465-5182585 3.55e-01 120 chrX:17830232-17830352 1.79e-01 31_[+5(5.00e-05)]_81 chr3R:29725652-29725772 5.45e-01 120 chrX:17176689-17176809 8.23e-01 120 chr3R:29088351-29088471 1.18e-01 23_[+2(2.77e-05)]_89 chrX:11146944-11147064 9.02e-01 120 chrX:18512331-18512451 7.92e-03 77_[+4(1.25e-05)]_35 chr3L:22136061-22136181 2.62e-02 50_[+3(9.23e-05)]_62 chr2R:9929532-9929652 9.17e-02 54_[+2(1.38e-05)]_58 chr3L:7634939-7635059 5.37e-01 120 chr2L:20078907-20079027 2.21e-01 120 chr3R:29699317-29699437 7.68e-01 120 chrX:17768377-17768497 7.73e-02 28_[+1(1.40e-05)]_2_[+1(7.16e-05)]_\ 50_[+1(1.40e-05)]_16 chr2R:14008405-14008525 1.63e-02 17_[+1(1.40e-05)]_21_[+1(1.40e-05)]_\ 66 chr3R:23942858-23942978 7.92e-01 120 chr3R:15920858-15920978 9.69e-03 23_[+2(1.38e-05)]_89 chr3R:30563318-30563438 7.06e-01 120 chrX:7110265-7110385 2.69e-02 120 chr2R:8327279-8327399 4.16e-05 6_[+3(4.62e-05)]_15_[+1(1.40e-05)]_\ 44_[+5(3.36e-05)]_15_[+5(5.00e-05)]_8 chr3R:10024188-10024308 1.60e-01 112_[+1(2.87e-05)] chr3L:12804991-12805111 6.40e-01 120 chrX:6663280-6663400 2.63e-01 120 chr2R:24571644-24571764 1.49e-01 120 chr2R:17458938-17459058 8.22e-01 120 chr3R:19096934-19097054 3.90e-01 120 chr2L:4403166-4403286 5.18e-01 120 chr3R:14356732-14356852 4.90e-01 120 chr2L:9449031-9449151 9.46e-01 120 chr3L:6752333-6752453 4.03e-01 120 chr3L:19132740-19132860 7.49e-03 120 chr2L:18320092-18320212 2.07e-01 51_[+1(5.74e-05)]_61 chr3R:6678616-6678736 1.96e-02 89_[+1(1.40e-05)]_23 chr2R:22561984-22562104 4.71e-01 120 chr2R:9543669-9543789 9.23e-01 120 chr3L:378157-378277 8.43e-07 11_[+1(1.40e-05)]_22_[+2(1.38e-05)]_\ 19_[+3(9.23e-05)]_4_[+3(9.23e-05)]_[+3(9.23e-05)]_7_[+5(3.36e-05)]_9 chr3L:9509280-9509400 1.31e-03 2_[+3(1.52e-05)]_65_[+1(2.87e-05)]_\ 37 chr3L:16806507-16806627 1.76e-02 48_[+3(3.02e-05)]_64 chr2R:21659877-21659997 4.22e-02 63_[+5(1.66e-05)]_49 chr2R:20111258-20111378 3.57e-04 43_[+3(6.17e-05)]_2_[+2(2.77e-05)]_\ 59 chr2R:15613852-15613972 1.98e-02 53_[+1(7.16e-05)]_59 chr3R:25652204-25652324 6.01e-01 120 chr2L:12586995-12587115 2.98e-01 51_[+3(4.62e-05)]_51_[+3(9.23e-05)]_\ 2 chr3L:8440982-8441102 8.73e-03 37_[+5(3.36e-05)]_75 chr2R:24305999-24306119 7.88e-01 120 chr2L:20066472-20066592 8.81e-01 120 chr3L:21011126-21011246 1.02e-01 22_[+3(1.52e-05)]_72_[+3(6.17e-05)]_\ 10 chr2L:20148552-20148672 5.88e-01 120 chr2R:9548186-9548306 6.77e-02 65_[+1(7.16e-05)]_[+1(7.16e-05)]_\ [+1(1.40e-05)]_31 chr3R:25215219-25215339 3.33e-02 82_[+5(1.66e-05)]_30 chr3R:11993226-11993346 4.46e-01 120 chrX:18517657-18517777 8.38e-01 120 chr3R:8784921-8785041 9.46e-01 120 chr3R:11157127-11157247 5.70e-01 120 chr3R:31311118-31311238 2.77e-01 120 chr3R:21850236-21850356 9.89e-01 120 chr3R:18315391-18315511 2.31e-01 120 chrX:618802-618922 4.22e-01 120 chr3L:16760410-16760530 4.06e-01 120 chrX:5517308-5517428 7.83e-01 120 chrX:3779891-3780011 5.02e-02 2_[+1(8.66e-05)]_110 chr2L:22024587-22024707 8.33e-01 120 chr3L:11708252-11708372 3.88e-01 120 chr2R:19291987-19292107 3.80e-01 120 chr2R:9414334-9414454 3.11e-03 106_[+2(1.38e-05)]_6 chrX:18239460-18239580 9.39e-01 120 chr3R:9157934-9158054 3.45e-01 120 chrX:6279173-6279293 1.10e-01 120 chr2L:9634219-9634339 6.18e-02 52_[+3(1.52e-05)]_60 chrX:12221712-12221832 5.33e-02 120 chr3L:17949191-17949311 1.33e-01 23_[+3(1.52e-05)]_89 chr2L:13878922-13879042 3.23e-01 120 chr2R:18536731-18536851 7.47e-01 120 chr3R:31669384-31669504 8.57e-01 120 chr3R:22447405-22447525 7.53e-01 120 chr2L:6179165-6179285 2.32e-01 120 chr2R:18539948-18540068 2.54e-02 36_[+4(1.25e-05)]_76 chr2L:6956902-6957022 4.16e-01 120 chrX:1349379-1349499 7.21e-01 120 chr2L:7940831-7940951 2.16e-01 120 chr3L:22407729-22407849 8.49e-02 120 chrX:7703110-7703230 9.25e-01 120 chr3R:9055200-9055320 4.57e-02 72_[+1(8.66e-05)]_40 chrX:16683898-16684018 6.93e-01 120 chr2R:11469679-11469799 2.27e-01 120 chr3R:10203700-10203820 1.44e-01 120 chr2L:22019034-22019154 9.65e-03 45_[+3(1.52e-05)]_67 chr3R:25027766-25027886 9.27e-01 120 chr3R:16655595-16655715 8.25e-01 120 chr3R:32068158-32068278 8.85e-03 13_[+3(6.17e-05)]_99 chrX:6220055-6220175 1.20e-03 68_[+3(1.52e-05)]_22_[+2(1.38e-05)]_\ 14 chr2L:10967353-10967473 2.47e-01 51_[+3(4.62e-05)]_61 chr2R:12025161-12025281 3.94e-01 120 chr3R:22664419-22664539 5.90e-01 120 chr3L:14672740-14672860 8.69e-02 120 chr3R:12408322-12408442 6.72e-01 120 chr2L:15762612-15762732 2.78e-02 120 chr3R:4714154-4714274 6.11e-01 120 chr3R:5300730-5300850 6.04e-02 120 chr2R:22270856-22270976 5.17e-01 120 chrX:5312210-5312330 2.84e-02 36_[+5(3.36e-05)]_76 chr2R:13337209-13337329 2.13e-02 68_[+1(8.66e-05)]_44 chr3R:27245313-27245433 3.12e-01 120 chr2R:23746605-23746725 8.71e-01 120 chrX:6109995-6110115 4.84e-02 120 chr2R:9388578-9388698 8.64e-01 120 chr2R:7381600-7381720 1.92e-01 120 chrX:10738979-10739099 2.10e-01 7_[+3(9.23e-05)]_105 chrX:13332910-13333030 6.41e-01 120 chr3R:23922345-23922465 5.05e-01 120 chr2R:12274329-12274449 2.95e-01 120 chr2L:20822947-20823067 4.37e-01 120 chr2R:14913201-14913321 9.43e-01 120 chr3R:29089761-29089881 1.00e+00 120 chr3R:4996728-4996848 3.00e-01 120 chr2R:8018926-8019046 3.47e-02 120 chr2R:8649520-8649640 3.28e-03 38_[+3(4.62e-05)]_74 chrX:16967588-16967708 1.72e-01 120 chr3L:21276959-21277079 2.38e-02 36_[+5(8.36e-05)]_76 chrX:2340191-2340311 9.61e-01 120 chr2R:12705191-12705311 3.33e-02 75_[+5(5.00e-05)]_37 chr3R:10140400-10140520 8.77e-02 120 chr3L:18114495-18114615 4.60e-01 120 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (5) found. ******************************************************************************** CPU: c28n03.farnam.hpc.yale.internal ********************************************************************************