******************************************************************************** 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/NC2α.fasta CONTROL SEQUENCES= --none-- ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ chr3R:16338529-16338649 1.0000 120 chr3R:24589104-24589224 1.0000 120 chr3R:29255231-29255351 1.0000 120 chr3L:15336626-15336746 1.0000 120 chr3R:24057292-24057412 1.0000 120 chr3R:18122007-18122127 1.0000 120 chr2R:12780457-12780577 1.0000 120 chr3L:4227281-4227401 1.0000 120 chr2R:12174240-12174360 1.0000 120 chr2R:22136914-22137034 1.0000 120 chr2L:20148518-20148638 1.0000 120 chrX:8271352-8271472 1.0000 120 chr3R:26010923-26011043 1.0000 120 chrX:19153326-19153446 1.0000 120 chr2R:23567340-23567460 1.0000 120 chrX:6279214-6279334 1.0000 120 chr3L:1463776-1463896 1.0000 120 chr2L:20104595-20104715 1.0000 120 chr3R:28845155-28845275 1.0000 120 chr3L:11286698-11286818 1.0000 120 chr3L:18398374-18398494 1.0000 120 chr2R:20313573-20313693 1.0000 120 chr3R:9054334-9054454 1.0000 120 chrX:11137043-11137163 1.0000 120 chr2L:5944658-5944778 1.0000 120 chr2R:8242646-8242766 1.0000 120 chr2R:6494393-6494513 1.0000 120 chr3R:5016521-5016641 1.0000 120 chr3R:9057111-9057231 1.0000 120 chrX:10745337-10745457 1.0000 120 chr3R:22133803-22133923 1.0000 120 chr2R:20562339-20562459 1.0000 120 chrX:17357643-17357763 1.0000 120 chr3L:22407034-22407154 1.0000 120 chr3R:26017442-26017562 1.0000 120 chr2R:6938661-6938781 1.0000 120 chr3R:21660598-21660718 1.0000 120 chr3L:17530866-17530986 1.0000 120 chr3R:20635722-20635842 1.0000 120 chr3R:12369215-12369335 1.0000 120 chr3R:31059885-31060005 1.0000 120 chrX:19308111-19308231 1.0000 120 chr2L:2753211-2753331 1.0000 120 chr3R:13813009-13813129 1.0000 120 chr2L:3675936-3676056 1.0000 120 chr2R:11175506-11175626 1.0000 120 chr2L:5906963-5907083 1.0000 120 chr3R:23445385-23445505 1.0000 120 chr3R:29265210-29265330 1.0000 120 chr2L:6725937-6726057 1.0000 120 chr2R:17458407-17458527 1.0000 120 chr2L:10238242-10238362 1.0000 120 chr2R:7663864-7663984 1.0000 120 chrX:8924980-8925100 1.0000 120 chr3L:7858387-7858507 1.0000 120 chr2L:15333826-15333946 1.0000 120 chr2L:7544553-7544673 1.0000 120 chrX:3024668-3024788 1.0000 120 chr3R:6818715-6818835 1.0000 120 chr3L:16711986-16712106 1.0000 120 chr2L:18987056-18987176 1.0000 120 chr4:980250-980370 1.0000 120 chr3R:8813728-8813848 1.0000 120 chr2R:12034174-12034294 1.0000 120 chrX:7098038-7098158 1.0000 120 chr3R:28634765-28634885 1.0000 120 chr2R:7885923-7886043 1.0000 120 chr3L:623736-623856 1.0000 120 chr3L:9505160-9505280 1.0000 120 chr3L:8347466-8347586 1.0000 120 chr2R:18232748-18232868 1.0000 120 chrX:13755333-13755453 1.0000 120 chr3R:19094165-19094285 1.0000 120 chr2L:6956882-6957002 1.0000 120 chr3R:21856219-21856339 1.0000 120 chr2L:10221071-10221191 1.0000 120 chr3R:29841625-29841745 1.0000 120 chr2R:12025111-12025231 1.0000 120 chrX:14211385-14211505 1.0000 120 chr3R:32051844-32051964 1.0000 120 chr2R:17097357-17097477 1.0000 120 chr2L:6700797-6700917 1.0000 120 chrX:17298021-17298141 1.0000 120 chr3R:5264931-5265051 1.0000 120 chr2L:19059047-19059167 1.0000 120 chr3R:21850345-21850465 1.0000 120 chr3R:11567032-11567152 1.0000 120 chrX:10602417-10602537 1.0000 120 chr2R:21475030-21475150 1.0000 120 chr2R:10238183-10238303 1.0000 120 chr3L:11429674-11429794 1.0000 120 chr3R:11372821-11372941 1.0000 120 chr3L:15142527-15142647 1.0000 120 chr3L:224232-224352 1.0000 120 chr2L:7306953-7307073 1.0000 120 chr2R:13008241-13008361 1.0000 120 chr3R:19164919-19165039 1.0000 120 chr2L:8554337-8554457 1.0000 120 chr2L:901397-901517 1.0000 120 chr2R:12274381-12274501 1.0000 120 chr2L:13838759-13838879 1.0000 120 chr2L:3600994-3601114 1.0000 120 chr2R:23551107-23551227 1.0000 120 chr2L:4892102-4892222 1.0000 120 chr3L:16760354-16760474 1.0000 120 chr2L:13203956-13204076 1.0000 120 chr2R:19451516-19451636 1.0000 120 chr2R:24965079-24965199 1.0000 120 chr2L:7998835-7998955 1.0000 120 chr2L:901609-901729 1.0000 120 chr2L:13082261-13082381 1.0000 120 chr2L:16816070-16816190 1.0000 120 chr2R:12259376-12259496 1.0000 120 chr3R:10598169-10598289 1.0000 120 chrX:22837503-22837623 1.0000 120 chrX:13128081-13128201 1.0000 120 chr3L:10845291-10845411 1.0000 120 chr3R:22041813-22041933 1.0000 120 chrX:13404005-13404125 1.0000 120 chr2L:11417657-11417777 1.0000 120 chr2R:13482152-13482272 1.0000 120 chr3R:16431761-16431881 1.0000 120 chr3L:19000629-19000749 1.0000 120 chr3R:26006025-26006145 1.0000 120 chr3R:23943017-23943137 1.0000 120 chr2L:7339766-7339886 1.0000 120 chrX:11548787-11548907 1.0000 120 chr3R:21377327-21377447 1.0000 120 chr3R:31395292-31395412 1.0000 120 chr3L:7359970-7360090 1.0000 120 chr3R:20276148-20276268 1.0000 120 chr2R:8615278-8615398 1.0000 120 chr3R:18242731-18242851 1.0000 120 chr3L:16770015-16770135 1.0000 120 chr2R:15735253-15735373 1.0000 120 chrX:3357741-3357861 1.0000 120 chr3R:20263915-20264035 1.0000 120 chr2L:14376964-14377084 1.0000 120 chr3R:8819679-8819799 1.0000 120 chr3R:22147627-22147747 1.0000 120 chr2L:19159564-19159684 1.0000 120 chrX:15498984-15499104 1.0000 120 chrX:18774960-18775080 1.0000 120 chr3R:13051370-13051490 1.0000 120 chr3L:14190842-14190962 1.0000 120 chr3R:9055255-9055375 1.0000 120 chrX:3367386-3367506 1.0000 120 chr3L:14131772-14131892 1.0000 120 chr3L:129414-129534 1.0000 120 chr2L:10967411-10967531 1.0000 120 chr2L:11037957-11038077 1.0000 120 chr3L:8584236-8584356 1.0000 120 chr2L:7043210-7043330 1.0000 120 chr3R:20948106-20948226 1.0000 120 chr2L:8573060-8573180 1.0000 120 chr3R:30428004-30428124 1.0000 120 chrX:18635404-18635524 1.0000 120 chrX:4106076-4106196 1.0000 120 chr2R:8649510-8649630 1.0000 120 chr2R:11541272-11541392 1.0000 120 chr2R:18802358-18802478 1.0000 120 chr2L:18666052-18666172 1.0000 120 chr3R:7977709-7977829 1.0000 120 chr3L:5987778-5987898 1.0000 120 chr2R:11095296-11095416 1.0000 120 chr3R:17053974-17054094 1.0000 120 chr2L:18822968-18823088 1.0000 120 chr2L:10516519-10516639 1.0000 120 chr3R:19472342-19472462 1.0000 120 chr3L:6059194-6059314 1.0000 120 chr3R:9344814-9344934 1.0000 120 chr3R:6405826-6405946 1.0000 120 chr3L:1177157-1177277 1.0000 120 chr3L:9028170-9028290 1.0000 120 chr3L:1795343-1795463 1.0000 120 chr2L:3477382-3477502 1.0000 120 chr3R:16235618-16235738 1.0000 120 chrX:8650853-8650973 1.0000 120 chr2L:1428412-1428532 1.0000 120 chrX:15076139-15076259 1.0000 120 chrX:10582169-10582289 1.0000 120 chr3L:21536951-21537071 1.0000 120 chr3L:7356406-7356526 1.0000 120 chr2R:24028507-24028627 1.0000 120 chr2L:20950864-20950984 1.0000 120 chr3R:8233504-8233624 1.0000 120 chr3R:18366425-18366545 1.0000 120 chr3R:23314507-23314627 1.0000 120 chr3L:14555055-14555175 1.0000 120 chr4:446064-446184 1.0000 120 chr3L:14786256-14786376 1.0000 120 chr3R:29556262-29556382 1.0000 120 chr3L:14195830-14195950 1.0000 120 chr2R:23940165-23940285 1.0000 120 chr3L:8395779-8395899 1.0000 120 chr2L:222254-222374 1.0000 120 chr3R:15794532-15794652 1.0000 120 chr3R:23333948-23334068 1.0000 120 chr2L:13205446-13205566 1.0000 120 chr3L:642910-643030 1.0000 120 chr2R:17719360-17719480 1.0000 120 chr3R:17584125-17584245 1.0000 120 chr3L:21007859-21007979 1.0000 120 chr2R:11639674-11639794 1.0000 120 chr2R:24174592-24174712 1.0000 120 chr3L:5857084-5857204 1.0000 120 chr2L:20945334-20945454 1.0000 120 chr3L:813414-813534 1.0000 120 chrX:19770322-19770442 1.0000 120 chr3R:21065216-21065336 1.0000 120 chr3L:15715895-15716015 1.0000 120 chr2L:13215960-13216080 1.0000 120 chr3L:15728315-15728435 1.0000 120 chr3R:21270105-21270225 1.0000 120 chr2L:21370854-21370974 1.0000 120 chr3L:1295782-1295902 1.0000 120 chr2R:18514006-18514126 1.0000 120 chr2L:3566701-3566821 1.0000 120 chr3L:18114483-18114603 1.0000 120 chr3R:27273558-27273678 1.0000 120 chr3L:2466754-2466874 1.0000 120 chr3L:11534139-11534259 1.0000 120 chr2R:10096806-10096926 1.0000 120 chrX:9137320-9137440 1.0000 120 chr3L:14956430-14956550 1.0000 120 chr3R:11569069-11569189 1.0000 120 chr3L:11205889-11206009 1.0000 120 chr3R:15676356-15676476 1.0000 120 chr2L:14545433-14545553 1.0000 120 chr3L:19575812-19575932 1.0000 120 chr2R:18662407-18662527 1.0000 120 chr3R:22596542-22596662 1.0000 120 chr2R:18242057-18242177 1.0000 120 chrX:7333331-7333451 1.0000 120 chr3R:12718315-12718435 1.0000 120 chr2R:12878809-12878929 1.0000 120 chr2L:10339470-10339590 1.0000 120 chr3R:20830373-20830493 1.0000 120 chr3R:16186828-16186948 1.0000 120 chr2R:12019235-12019355 1.0000 120 chr2R:12605671-12605791 1.0000 120 chr3R:9870126-9870246 1.0000 120 chr3R:5613134-5613254 1.0000 120 chr3L:4138957-4139077 1.0000 120 chr3L:3767949-3768069 1.0000 120 chr2L:21237130-21237250 1.0000 120 chr3L:6264562-6264682 1.0000 120 chrX:21242013-21242133 1.0000 120 chr2R:8144784-8144904 1.0000 120 chr3R:26654738-26654858 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_NC2α/ -dna -nmotifs 5 -w 8 -maxsize 250000 -nostatus ../result/final_prediction/fly/fasta/RankLinear8.0_60/NC2α.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 0.278 C 0.223 G 0.221 T 0.278 Background letter frequencies (from file dataset with add-one prior applied): A 0.278 C 0.223 G 0.221 T 0.277 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF TTTGTTTK MEME-1 width = 8 sites = 52 llr = 418 E-value = 1.6e-001 ******************************************************************************** -------------------------------------------------------------------------------- Motif TTTGTTTK MEME-1 Description -------------------------------------------------------------------------------- Simplified A :::1:::: pos.-specific C 12:::::: probability G :::7:1:6 matrix T 98a2a9a4 bits 2.2 2.0 * * * 1.7 * * * 1.5 * * *** Relative 1.3 * * *** Entropy 1.1 *** **** (11.6 bits) 0.9 ******** 0.7 ******** 0.4 ******** 0.2 ******** 0.0 -------- Multilevel TTTGTTTG consensus T T sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTTGTTTK MEME-1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chrX:21242013-21242133 11 2.21e-05 GTGCGTGTGA TTTGTTTG TGCTGTTGAC chr3R:15676356-15676476 77 2.21e-05 GTGCCCACTG TTTGTTTG CCTTGTTTGC chr3L:642910-643030 47 2.21e-05 TATTTTATGC TTTGTTTG CCCATTACAA chr2L:7043210-7043330 22 2.21e-05 TTTGCCGATG TTTGTTTG CATTAGGTGT chr3R:8819679-8819799 83 2.21e-05 ACAAAAGGTG TTTGTTTG GCTATTCAAG chr2L:7339766-7339886 16 2.21e-05 AAGTCGTTGA TTTGTTTG CACTGACCCG chr2L:13838759-13838879 90 2.21e-05 GTCTGTTTGG TTTGTTTG TAAATAGCCA chr2R:12274381-12274501 91 2.21e-05 CCGGCTGCAT TTTGTTTG ACAGTTTTCC chr3R:8813728-8813848 5 2.21e-05 TTGT TTTGTTTG AGTTTTAACT chr2R:23567340-23567460 19 2.21e-05 GCTCCATTTG TTTGTTTG TATTCGCCTG chr3R:16338529-16338649 40 2.21e-05 GCTTATATAG TTTGTTTG CCAGTGTGGC chr3L:11534139-11534259 110 4.97e-05 GTTTTCTTAT TTTGTTTT GCT chr3R:21270105-21270225 71 4.97e-05 CACTTTCATA TTTGTTTT GGCCACCACT chr3L:7356406-7356526 70 4.97e-05 ACAAATTGGA TTTGTTTT GGTGGCGACC chr3R:9344814-9344934 90 4.97e-05 GTTATGCAAT TTTGTTTT GTCTGTCGGT chr3L:5987778-5987898 89 4.97e-05 GGATTGCACT TTTGTTTT CAACACAATT chr2R:13482152-13482272 88 4.97e-05 TTTTAGGATT TTTGTTTT ACTTTCTACG chr3R:19094165-19094285 78 4.97e-05 GACGTCCGAC TTTGTTTT CCGACTCGAT chrX:19308111-19308231 16 4.97e-05 tttttttttt tttgtttt tctttctttt chr2R:20562339-20562459 103 4.97e-05 TGAATTTGAT TTTGTTTT ATAATTACTT chr2R:22136914-22137034 62 4.97e-05 GTGTTCAATC TTTGTTTT CGTAGCGCGG chr3R:22041813-22041933 5 6.75e-05 CAAC TCTGTTTG TGCGGAGTGG chr2L:6700797-6700917 48 6.75e-05 AGCCACTTGC TCTGTTTG CCCACAAACA chr3L:11205889-11206009 32 9.51e-05 ACTAGTTGCA TTTTTTTG TGCTAAATGC chrX:18774960-18775080 19 9.51e-05 AACATCTGGC TTTTTTTG GTGTTTCCGA chrX:13128081-13128201 4 9.51e-05 ttt tttttttG TCATGAGTTA chrX:3024668-3024788 69 9.51e-05 CCCCCttgtg tttttttg ttcggtgttt chrX:8271352-8271472 85 9.51e-05 TTTATGTGTT TTTTTTTG TTATTGCGGT chr3R:9870126-9870246 74 1.17e-04 AAAACTGTTG TCTGTTTT TCACCAGAAT chr3R:12718315-12718435 102 1.17e-04 ACATTAAAAC TCTGTTTT TTCAGTGCAA chrX:7333331-7333451 109 1.17e-04 AATTTTCAAA TCTGTTTT GTGT chr3L:14195830-14195950 87 1.17e-04 TTTCAGTGTG TCTGTTTT TTGTGGGCGT chrX:15076139-15076259 7 1.17e-04 AAGCAC TCTGTTTT ATTTTATTCC chr3R:26654738-26654858 42 1.52e-04 ATGAAGACGT TTTTTTTT AGCAATTTCG chr3R:16235618-16235738 86 1.52e-04 GGAAAAAGAA TTTTTTTT ATAGGTATTA chrX:3357741-3357861 1 1.52e-04 . tttttttt tCCTTTATCA chr3L:15728315-15728435 37 1.80e-04 TTTCGGGTTT TTTATTTG CCGTAGAGTT chr3R:19164919-19165039 30 1.80e-04 GCATGTTTTA TTTATTTG CCTTATTGGT chr2L:5906963-5907083 17 1.80e-04 ATCGGTCTTG TTTATTTG CTTATCAGTA chr3R:22596542-22596662 23 2.15e-04 AATCAATCGC CTTGTTTG CCACCACCca chr3L:15715895-15716015 36 2.15e-04 CCGTGCTCGC CTTGTTTG CCCTACGTTA chr3R:7977709-7977829 32 2.15e-04 AAATGCCTCG TTTGTGTG GTATGTAAAA chr2L:2753211-2753331 33 2.15e-04 ATTCAGTGTG TTTGTGTG CTTCGTTCGG chr3R:21660598-21660718 99 2.15e-04 CAACTGGCCG TTTGTGTG TGCGTGTGTG chr3L:21007859-21007979 26 2.72e-04 CACTGCTTCT TCTTTTTG TCTTCGTTGG chr3R:9057111-9057231 35 2.72e-04 ATTTTTGAAT TTTATTTT GAAATCGAAC chrX:6279214-6279334 4 2.72e-04 GCT TTTATTTT ACTTGCTCGG chrX:10582169-10582289 71 2.90e-04 TGTGTCTGTC TGTGTTTG GAAACTAAAC chrX:11137043-11137163 57 2.90e-04 AATCAGCCGT TGTGTTTG AAAAGTGAGA chr3R:13051370-13051490 10 3.34e-04 TATACGTCT CTTGTTTT TCTTACTTTT chr3R:9055255-9055375 45 3.62e-04 GCGCTGGGTA TCTTTTTT CTTATCCTAT chr3R:23943017-23943137 28 3.62e-04 GGGTTCCAAC TCTTTTTT TATTCTGTTC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTTGTTTK MEME-1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrX:21242013-21242133 2.2e-05 10_[+1]_102 chr3R:15676356-15676476 2.2e-05 76_[+1]_36 chr3L:642910-643030 2.2e-05 46_[+1]_66 chr2L:7043210-7043330 2.2e-05 21_[+1]_91 chr3R:8819679-8819799 2.2e-05 82_[+1]_30 chr2L:7339766-7339886 2.2e-05 15_[+1]_97 chr2L:13838759-13838879 2.2e-05 89_[+1]_23 chr2R:12274381-12274501 2.2e-05 90_[+1]_22 chr3R:8813728-8813848 2.2e-05 4_[+1]_108 chr2R:23567340-23567460 2.2e-05 18_[+1]_94 chr3R:16338529-16338649 2.2e-05 39_[+1]_73 chr3L:11534139-11534259 5e-05 109_[+1]_3 chr3R:21270105-21270225 5e-05 70_[+1]_42 chr3L:7356406-7356526 5e-05 69_[+1]_43 chr3R:9344814-9344934 5e-05 89_[+1]_23 chr3L:5987778-5987898 5e-05 88_[+1]_24 chr2R:13482152-13482272 5e-05 87_[+1]_25 chr3R:19094165-19094285 5e-05 77_[+1]_35 chrX:19308111-19308231 5e-05 15_[+1]_97 chr2R:20562339-20562459 5e-05 102_[+1]_10 chr2R:22136914-22137034 5e-05 61_[+1]_51 chr3R:22041813-22041933 6.7e-05 4_[+1]_108 chr2L:6700797-6700917 6.7e-05 47_[+1]_65 chr3L:11205889-11206009 9.5e-05 31_[+1]_81 chrX:18774960-18775080 9.5e-05 18_[+1]_94 chrX:13128081-13128201 9.5e-05 3_[+1]_109 chrX:3024668-3024788 9.5e-05 68_[+1]_44 chrX:8271352-8271472 9.5e-05 84_[+1]_28 chr3R:9870126-9870246 0.00012 73_[+1]_39 chr3R:12718315-12718435 0.00012 101_[+1]_11 chrX:7333331-7333451 0.00012 108_[+1]_4 chr3L:14195830-14195950 0.00012 86_[+1]_26 chrX:15076139-15076259 0.00012 6_[+1]_106 chr3R:26654738-26654858 0.00015 41_[+1]_71 chr3R:16235618-16235738 0.00015 85_[+1]_27 chrX:3357741-3357861 0.00015 [+1]_112 chr3L:15728315-15728435 0.00018 36_[+1]_76 chr3R:19164919-19165039 0.00018 29_[+1]_83 chr2L:5906963-5907083 0.00018 16_[+1]_96 chr3R:22596542-22596662 0.00022 22_[+1]_90 chr3L:15715895-15716015 0.00022 35_[+1]_77 chr3R:7977709-7977829 0.00022 31_[+1]_81 chr2L:2753211-2753331 0.00022 32_[+1]_80 chr3R:21660598-21660718 0.00022 98_[+1]_14 chr3L:21007859-21007979 0.00027 25_[+1]_87 chr3R:9057111-9057231 0.00027 34_[+1]_78 chrX:6279214-6279334 0.00027 3_[+1]_109 chrX:10582169-10582289 0.00029 70_[+1]_42 chrX:11137043-11137163 0.00029 56_[+1]_56 chr3R:13051370-13051490 0.00033 9_[+1]_103 chr3R:9055255-9055375 0.00036 44_[+1]_68 chr3R:23943017-23943137 0.00036 27_[+1]_85 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTTGTTTK MEME-1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF TTTGTTTK width=8 seqs=52 chrX:21242013-21242133 ( 11) TTTGTTTG 1 chr3R:15676356-15676476 ( 77) TTTGTTTG 1 chr3L:642910-643030 ( 47) TTTGTTTG 1 chr2L:7043210-7043330 ( 22) TTTGTTTG 1 chr3R:8819679-8819799 ( 83) TTTGTTTG 1 chr2L:7339766-7339886 ( 16) TTTGTTTG 1 chr2L:13838759-13838879 ( 90) TTTGTTTG 1 chr2R:12274381-12274501 ( 91) TTTGTTTG 1 chr3R:8813728-8813848 ( 5) TTTGTTTG 1 chr2R:23567340-23567460 ( 19) TTTGTTTG 1 chr3R:16338529-16338649 ( 40) TTTGTTTG 1 chr3L:11534139-11534259 ( 110) TTTGTTTT 1 chr3R:21270105-21270225 ( 71) TTTGTTTT 1 chr3L:7356406-7356526 ( 70) TTTGTTTT 1 chr3R:9344814-9344934 ( 90) TTTGTTTT 1 chr3L:5987778-5987898 ( 89) TTTGTTTT 1 chr2R:13482152-13482272 ( 88) TTTGTTTT 1 chr3R:19094165-19094285 ( 78) TTTGTTTT 1 chrX:19308111-19308231 ( 16) TTTGTTTT 1 chr2R:20562339-20562459 ( 103) TTTGTTTT 1 chr2R:22136914-22137034 ( 62) TTTGTTTT 1 chr3R:22041813-22041933 ( 5) TCTGTTTG 1 chr2L:6700797-6700917 ( 48) TCTGTTTG 1 chr3L:11205889-11206009 ( 32) TTTTTTTG 1 chrX:18774960-18775080 ( 19) TTTTTTTG 1 chrX:13128081-13128201 ( 4) TTTTTTTG 1 chrX:3024668-3024788 ( 69) TTTTTTTG 1 chrX:8271352-8271472 ( 85) TTTTTTTG 1 chr3R:9870126-9870246 ( 74) TCTGTTTT 1 chr3R:12718315-12718435 ( 102) TCTGTTTT 1 chrX:7333331-7333451 ( 109) TCTGTTTT 1 chr3L:14195830-14195950 ( 87) TCTGTTTT 1 chrX:15076139-15076259 ( 7) TCTGTTTT 1 chr3R:26654738-26654858 ( 42) TTTTTTTT 1 chr3R:16235618-16235738 ( 86) TTTTTTTT 1 chrX:3357741-3357861 ( 1) TTTTTTTT 1 chr3L:15728315-15728435 ( 37) TTTATTTG 1 chr3R:19164919-19165039 ( 30) TTTATTTG 1 chr2L:5906963-5907083 ( 17) TTTATTTG 1 chr3R:22596542-22596662 ( 23) CTTGTTTG 1 chr3L:15715895-15716015 ( 36) CTTGTTTG 1 chr3R:7977709-7977829 ( 32) TTTGTGTG 1 chr2L:2753211-2753331 ( 33) TTTGTGTG 1 chr3R:21660598-21660718 ( 99) TTTGTGTG 1 chr3L:21007859-21007979 ( 26) TCTTTTTG 1 chr3R:9057111-9057231 ( 35) TTTATTTT 1 chrX:6279214-6279334 ( 4) TTTATTTT 1 chrX:10582169-10582289 ( 71) TGTGTTTG 1 chrX:11137043-11137163 ( 57) TGTGTTTG 1 chr3R:13051370-13051490 ( 10) CTTGTTTT 1 chr3R:9055255-9055375 ( 45) TCTTTTTT 1 chr3R:23943017-23943137 ( 28) TCTTTTTT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTTGTTTK MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 28250 bayes= 10.2487 E= 1.6e-001 -1234 -195 -1234 176 -1234 -21 -252 147 -1234 -1234 -1234 185 -153 -1234 164 -39 -1234 -1234 -1234 185 -1234 -1234 -194 176 -1234 -1234 -1234 185 -1234 -1234 133 67 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTTGTTTK MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 52 E= 1.6e-001 0.000000 0.057692 0.000000 0.942308 0.000000 0.192308 0.038462 0.769231 0.000000 0.000000 0.000000 1.000000 0.096154 0.000000 0.692308 0.211538 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.057692 0.942308 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.557692 0.442308 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTTGTTTK MEME-1 regular expression -------------------------------------------------------------------------------- TTT[GT]TTT[GT] -------------------------------------------------------------------------------- Time 7.42 secs. ******************************************************************************** ******************************************************************************** MOTIF GCCRGCWG MEME-2 width = 8 sites = 30 llr = 270 E-value = 1.4e-001 ******************************************************************************** -------------------------------------------------------------------------------- Motif GCCRGCWG MEME-2 Description -------------------------------------------------------------------------------- Simplified A :::3::3: pos.-specific C :7a2:a2: probability G a::5a::a matrix T :3::::5: bits 2.2 * * ** * 2.0 * * ** * 1.7 * * ** * 1.5 * * ** * Relative 1.3 *** ** * Entropy 1.1 *** ** * (13.0 bits) 0.9 *** ** * 0.7 *** ** * 0.4 ******** 0.2 ******** 0.0 -------- Multilevel GCCGGCTG consensus T A A sequence C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCCRGCWG MEME-2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr3L:14555055-14555175 33 7.33e-06 TCACGTTTTC GCCGGCTG CCTCAGATAC chr3R:11567032-11567152 35 7.33e-06 TCTGCGGCGT GCCGGCTG TTATATACTT chr3R:12369215-12369335 83 7.33e-06 TTTTATAGGG GCCGGCTG TGGTCGCCAC chr3R:26017442-26017562 111 7.33e-06 GAAATCGTAC GCCGGCTG AT chr2R:6494393-6494513 7 7.33e-06 ACCGCT GCCGGCTG CGAAGTGATC chr3L:1463776-1463896 17 7.33e-06 ACTTATAAAG GCCGGCTG CCTTGCCTTT chr2L:7043210-7043330 4 1.65e-05 AAA GCCAGCTG TTTGCCGATG chr3L:8347466-8347586 88 1.65e-05 GTTGCCCAAC GCCAGCTG TGCACACAAC chr2L:6725937-6726057 105 1.65e-05 CGGGCGTGGT GCCAGCTG GCGTGGGC chr3R:13813009-13813129 40 2.39e-05 CGACAGCGAC GCCGGCAG CGACGTCGAG chrX:8924980-8925100 90 2.98e-05 AGCCGAAGTT GCCGGCCG ATTGCTGGCC chr2L:21370854-21370974 94 3.72e-05 CGAAGTTATC GCCCGCTG TATTATCAGC chr2R:8649510-8649630 31 3.72e-05 GCACACAGAC GCCCGCTG GGCAagagag chr2L:10339470-10339590 36 5.55e-05 GTTATTGCCA GCCAGCAG CATGTTGGAG chr3L:14786256-14786376 24 5.55e-05 CTGTTTGTCG GTCGGCTG GAAAAATTAC chr3R:9344814-9344934 35 5.55e-05 TCTTCTTTTT GTCGGCTG TCGTTGTTTT chr3L:16770015-16770135 109 5.55e-05 GAGGTAGGAA GCCAGCAG GAAA chr3R:26006025-26006145 1 5.55e-05 . GTCGGCTG GCTCTGGGAT chr2R:13008241-13008361 8 5.55e-05 CGCCAGT GTCGGCTG CACTGTAAAC chr2R:12034174-12034294 4 5.55e-05 ATC GCCAGCAG GAGAAAAACA chr2L:10516519-10516639 10 6.30e-05 AGAACCAGC GCCAGCCG GGTTTCGTCA chr2R:23567340-23567460 36 6.30e-05 GTATTCGCCT GCCAGCCG GCAAGCAAGT chr2L:2753211-2753331 6 7.04e-05 AGACG GCCCGCAG CTGAATCGCA chr2L:13205446-13205566 13 8.78e-05 GACTGTGGCT GCCCGCCG GTCGTCCGTC chr3L:17530866-17530986 69 8.78e-05 GACGTGCCAC GCCCGCCG CCCCGCCGGC chr2L:19159564-19159684 97 9.69e-05 TTCGATTCGC GTCGGCAG CGACTGtgtt chr3L:22407034-22407154 34 1.04e-04 GAGGTCCGTC GTCGGCCG CCCGTGGCCG chr3R:6405826-6405946 113 1.25e-04 GTCCGAAAGT GTCAGCAG chr2L:20148518-20148638 109 1.25e-04 GTATTTAGTA GTCAGCAG CGAA chr3L:8395779-8395899 91 1.43e-04 TCAGTGTATG GCCTGCTG GTGCTGCTGT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCCRGCWG MEME-2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr3L:14555055-14555175 7.3e-06 32_[+2]_80 chr3R:11567032-11567152 7.3e-06 34_[+2]_78 chr3R:12369215-12369335 7.3e-06 82_[+2]_30 chr3R:26017442-26017562 7.3e-06 110_[+2]_2 chr2R:6494393-6494513 7.3e-06 6_[+2]_106 chr3L:1463776-1463896 7.3e-06 16_[+2]_96 chr2L:7043210-7043330 1.7e-05 3_[+2]_109 chr3L:8347466-8347586 1.7e-05 87_[+2]_25 chr2L:6725937-6726057 1.7e-05 104_[+2]_8 chr3R:13813009-13813129 2.4e-05 39_[+2]_73 chrX:8924980-8925100 3e-05 89_[+2]_23 chr2L:21370854-21370974 3.7e-05 93_[+2]_19 chr2R:8649510-8649630 3.7e-05 30_[+2]_82 chr2L:10339470-10339590 5.6e-05 35_[+2]_77 chr3L:14786256-14786376 5.6e-05 23_[+2]_89 chr3R:9344814-9344934 5.6e-05 34_[+2]_78 chr3L:16770015-16770135 5.6e-05 108_[+2]_4 chr3R:26006025-26006145 5.6e-05 [+2]_112 chr2R:13008241-13008361 5.6e-05 7_[+2]_105 chr2R:12034174-12034294 5.6e-05 3_[+2]_109 chr2L:10516519-10516639 6.3e-05 9_[+2]_103 chr2R:23567340-23567460 6.3e-05 35_[+2]_77 chr2L:2753211-2753331 7e-05 5_[+2]_107 chr2L:13205446-13205566 8.8e-05 12_[+2]_100 chr3L:17530866-17530986 8.8e-05 68_[+2]_44 chr2L:19159564-19159684 9.7e-05 96_[+2]_16 chr3L:22407034-22407154 0.0001 33_[+2]_79 chr3R:6405826-6405946 0.00012 112_[+2] chr2L:20148518-20148638 0.00012 108_[+2]_4 chr3L:8395779-8395899 0.00014 90_[+2]_22 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCCRGCWG MEME-2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF GCCRGCWG width=8 seqs=30 chr3L:14555055-14555175 ( 33) GCCGGCTG 1 chr3R:11567032-11567152 ( 35) GCCGGCTG 1 chr3R:12369215-12369335 ( 83) GCCGGCTG 1 chr3R:26017442-26017562 ( 111) GCCGGCTG 1 chr2R:6494393-6494513 ( 7) GCCGGCTG 1 chr3L:1463776-1463896 ( 17) GCCGGCTG 1 chr2L:7043210-7043330 ( 4) GCCAGCTG 1 chr3L:8347466-8347586 ( 88) GCCAGCTG 1 chr2L:6725937-6726057 ( 105) GCCAGCTG 1 chr3R:13813009-13813129 ( 40) GCCGGCAG 1 chrX:8924980-8925100 ( 90) GCCGGCCG 1 chr2L:21370854-21370974 ( 94) GCCCGCTG 1 chr2R:8649510-8649630 ( 31) GCCCGCTG 1 chr2L:10339470-10339590 ( 36) GCCAGCAG 1 chr3L:14786256-14786376 ( 24) GTCGGCTG 1 chr3R:9344814-9344934 ( 35) GTCGGCTG 1 chr3L:16770015-16770135 ( 109) GCCAGCAG 1 chr3R:26006025-26006145 ( 1) GTCGGCTG 1 chr2R:13008241-13008361 ( 8) GTCGGCTG 1 chr2R:12034174-12034294 ( 4) GCCAGCAG 1 chr2L:10516519-10516639 ( 10) GCCAGCCG 1 chr2R:23567340-23567460 ( 36) GCCAGCCG 1 chr2L:2753211-2753331 ( 6) GCCCGCAG 1 chr2L:13205446-13205566 ( 13) GCCCGCCG 1 chr3L:17530866-17530986 ( 69) GCCCGCCG 1 chr2L:19159564-19159684 ( 97) GTCGGCAG 1 chr3L:22407034-22407154 ( 34) GTCGGCCG 1 chr3R:6405826-6405946 ( 113) GTCAGCAG 1 chr2L:20148518-20148638 ( 109) GTCAGCAG 1 chr3L:8395779-8395899 ( 91) GCCTGCTG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCCRGCWG MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 28250 bayes= 11.1531 E= 1.4e-001 -1155 -1155 218 -1155 -1155 172 -1155 -6 -1155 216 -1155 -1155 26 -42 108 -305 -1155 -1155 218 -1155 -1155 216 -1155 -1155 -6 -16 -1155 94 -1155 -1155 218 -1155 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCCRGCWG MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 30 E= 1.4e-001 0.000000 0.000000 1.000000 0.000000 0.000000 0.733333 0.000000 0.266667 0.000000 1.000000 0.000000 0.000000 0.333333 0.166667 0.466667 0.033333 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.266667 0.200000 0.000000 0.533333 0.000000 0.000000 1.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCCRGCWG MEME-2 regular expression -------------------------------------------------------------------------------- G[CT]C[GA]GC[TAC]G -------------------------------------------------------------------------------- Time 13.68 secs. ******************************************************************************** ******************************************************************************** MOTIF CGKTGCGG MEME-3 width = 8 sites = 8 llr = 88 E-value = 1.3e+004 ******************************************************************************** -------------------------------------------------------------------------------- Motif CGKTGCGG MEME-3 Description -------------------------------------------------------------------------------- Simplified A :::::::: pos.-specific C a::::a:: probability G :a5:a:aa matrix T ::5a:::: bits 2.2 ** **** 2.0 ** ***** 1.7 ** ***** 1.5 ** ***** Relative 1.3 ** ***** Entropy 1.1 ******** (15.9 bits) 0.9 ******** 0.7 ******** 0.4 ******** 0.2 ******** 0.0 -------- Multilevel CGGTGCGG consensus T sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CGKTGCGG MEME-3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr3L:6059194-6059314 25 7.26e-06 AGGAGGCAAG CGGTGCGG AAGTGGGTTA chrX:15498984-15499104 108 7.26e-06 CTGCTCGCGT CGGTGCGG CGTTG chr3L:7359970-7360090 15 7.26e-06 ACTTCACGTG CGGTGCGG GTAACTTCAT chr2L:2753211-2753331 48 7.26e-06 GTGCTTCGTT CGGTGCGG TTCTCTCTGT chr2R:12259376-12259496 54 1.64e-05 AGTCGTCGAC CGTTGCGG ACGGAAATTC chr3R:11567032-11567152 56 1.64e-05 TATACTTTCG CGTTGCGG CTACGGCATT chr3R:32051844-32051964 80 1.64e-05 TATATGTGTG CGTTGCGG GACTTGTGCT chr3L:15336626-15336746 61 1.64e-05 AAGTTGCGCA CGTTGCGG CAGTCAGTCG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CGKTGCGG MEME-3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr3L:6059194-6059314 7.3e-06 24_[+3]_88 chrX:15498984-15499104 7.3e-06 107_[+3]_5 chr3L:7359970-7360090 7.3e-06 14_[+3]_98 chr2L:2753211-2753331 7.3e-06 47_[+3]_65 chr2R:12259376-12259496 1.6e-05 53_[+3]_59 chr3R:11567032-11567152 1.6e-05 55_[+3]_57 chr3R:32051844-32051964 1.6e-05 79_[+3]_33 chr3L:15336626-15336746 1.6e-05 60_[+3]_52 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CGKTGCGG MEME-3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF CGKTGCGG width=8 seqs=8 chr3L:6059194-6059314 ( 25) CGGTGCGG 1 chrX:15498984-15499104 ( 108) CGGTGCGG 1 chr3L:7359970-7360090 ( 15) CGGTGCGG 1 chr2L:2753211-2753331 ( 48) CGGTGCGG 1 chr2R:12259376-12259496 ( 54) CGTTGCGG 1 chr3R:11567032-11567152 ( 56) CGTTGCGG 1 chr3R:32051844-32051964 ( 80) CGTTGCGG 1 chr3L:15336626-15336746 ( 61) CGTTGCGG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CGKTGCGG MEME-3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 28250 bayes= 12.5227 E= 1.3e+004 -965 216 -965 -965 -965 -965 217 -965 -965 -965 117 85 -965 -965 -965 185 -965 -965 217 -965 -965 216 -965 -965 -965 -965 217 -965 -965 -965 217 -965 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CGKTGCGG MEME-3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 8 E= 1.3e+004 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.500000 0.500000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CGKTGCGG MEME-3 regular expression -------------------------------------------------------------------------------- CG[GT]TGCGG -------------------------------------------------------------------------------- Time 19.87 secs. ******************************************************************************** ******************************************************************************** MOTIF GCGAGCGR MEME-4 width = 8 sites = 8 llr = 86 E-value = 5.7e+004 ******************************************************************************** -------------------------------------------------------------------------------- Motif GCGAGCGR MEME-4 Description -------------------------------------------------------------------------------- Simplified A :::a:::4 pos.-specific C :a:::a:1 probability G a:a:a:a5 matrix T :::::::: bits 2.2 *** *** 2.0 *** *** 1.7 ******* 1.5 ******* Relative 1.3 ******* Entropy 1.1 ******* (15.5 bits) 0.9 ******* 0.7 ******** 0.4 ******** 0.2 ******** 0.0 -------- Multilevel GCGAGCGG consensus A sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCGAGCGR MEME-4 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr3R:26006025-26006145 63 7.29e-06 GACAGTGAGT GCGAGCGG GACACTCATT chr2R:18232748-18232868 40 7.29e-06 GAATCTCGAA GCGAGCGG TACGCAGGCG chr2L:6725937-6726057 8 7.29e-06 AAGGTGC GCGAGCGG TTGCGGCTTT chr3L:17530866-17530986 85 7.29e-06 CGCCCCGCCG GCGAGCGG CCTCTGTTGC chr3L:14131772-14131892 59 1.65e-05 GCGTGGGAGT GCGAGCGA GATAAACGGA chr2R:12025111-12025231 69 1.65e-05 CGGGGATCTT GCGAGCGA TTCGGTTTCA chr2R:22136914-22137034 6 1.65e-05 GCGAC GCGAGCGA GAGAGGCAAA chr3L:1463776-1463896 58 2.38e-05 CGTGCGAGCC GCGAGCGC GAGATCATCA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCGAGCGR MEME-4 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr3R:26006025-26006145 7.3e-06 62_[+4]_50 chr2R:18232748-18232868 7.3e-06 39_[+4]_73 chr2L:6725937-6726057 7.3e-06 7_[+4]_105 chr3L:17530866-17530986 7.3e-06 84_[+4]_28 chr3L:14131772-14131892 1.6e-05 58_[+4]_54 chr2R:12025111-12025231 1.6e-05 68_[+4]_44 chr2R:22136914-22137034 1.6e-05 5_[+4]_107 chr3L:1463776-1463896 2.4e-05 57_[+4]_55 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCGAGCGR MEME-4 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF GCGAGCGR width=8 seqs=8 chr3R:26006025-26006145 ( 63) GCGAGCGG 1 chr2R:18232748-18232868 ( 40) GCGAGCGG 1 chr2L:6725937-6726057 ( 8) GCGAGCGG 1 chr3L:17530866-17530986 ( 85) GCGAGCGG 1 chr3L:14131772-14131892 ( 59) GCGAGCGA 1 chr2R:12025111-12025231 ( 69) GCGAGCGA 1 chr2R:22136914-22137034 ( 6) GCGAGCGA 1 chr3L:1463776-1463896 ( 58) GCGAGCGC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCGAGCGR MEME-4 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 28250 bayes= 13.1077 E= 5.7e+004 -965 -965 217 -965 -965 216 -965 -965 -965 -965 217 -965 184 -965 -965 -965 -965 -965 217 -965 -965 216 -965 -965 -965 -965 217 -965 43 -83 117 -965 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCGAGCGR MEME-4 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 8 E= 5.7e+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 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.375000 0.125000 0.500000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCGAGCGR MEME-4 regular expression -------------------------------------------------------------------------------- GCGAGCG[GA] -------------------------------------------------------------------------------- Time 26.04 secs. ******************************************************************************** ******************************************************************************** MOTIF TGYTGTTG MEME-5 width = 8 sites = 13 llr = 128 E-value = 1.1e+005 ******************************************************************************** -------------------------------------------------------------------------------- Motif TGYTGTTG MEME-5 Description -------------------------------------------------------------------------------- Simplified A :::::::: pos.-specific C ::5::2:: probability G :a::a::a matrix T a:5a:8a: bits 2.2 * * * 2.0 ** ** ** 1.7 ** ** ** 1.5 ** ** ** Relative 1.3 ** ** ** Entropy 1.1 ******** (14.2 bits) 0.9 ******** 0.7 ******** 0.4 ******** 0.2 ******** 0.0 -------- Multilevel TGTTGTTG consensus C C sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TGYTGTTG MEME-5 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chrX:21242013-21242133 19 1.42e-05 GATTTGTTTG TGCTGTTG ACTTTGGATA chr3L:8395779-8395899 103 1.42e-05 CTGCTGGTGC TGCTGTTG CGCGTTATTG chr3R:26006025-26006145 101 1.42e-05 CGCGGCCTGC TGCTGTTG CCAGCGGTGG chr2R:12019235-12019355 16 3.18e-05 CCGGGGATGG TGTTGTTG GTGGTGGTGA chr3R:22596542-22596662 108 3.18e-05 GTGGGCGTCG TGTTGTTG CTATT chrX:22837503-22837623 70 3.18e-05 AACGTCTGTG TGTTGTTG ACATTACAAG chr2L:13082261-13082381 13 3.18e-05 CGTAAGATAT TGTTGTTG CTGCTTTCCT chr2R:17458407-17458527 79 3.18e-05 TGGGACTGGT TGTTGTTG TACATAACGG chrX:19308111-19308231 51 3.18e-05 TGTTTGCATT TGTTGTTG CGCCGCCTTG chr3R:28845155-28845275 110 3.18e-05 TCCCGAATTT TGTTGTTG TTC chr2L:3600994-3601114 69 4.32e-05 AGAAATCCAT TGCTGCTG GAAAACAGCT chr3R:26017442-26017562 28 4.32e-05 CGTTTACTGA TGCTGCTG CGCCGGCGTC chr3R:5016521-5016641 12 4.32e-05 CTTGTGCTCC TGCTGCTG CCACCACCGC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TGYTGTTG MEME-5 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrX:21242013-21242133 1.4e-05 18_[+5]_94 chr3L:8395779-8395899 1.4e-05 102_[+5]_10 chr3R:26006025-26006145 1.4e-05 100_[+5]_12 chr2R:12019235-12019355 3.2e-05 15_[+5]_97 chr3R:22596542-22596662 3.2e-05 107_[+5]_5 chrX:22837503-22837623 3.2e-05 69_[+5]_43 chr2L:13082261-13082381 3.2e-05 12_[+5]_100 chr2R:17458407-17458527 3.2e-05 78_[+5]_34 chrX:19308111-19308231 3.2e-05 50_[+5]_62 chr3R:28845155-28845275 3.2e-05 109_[+5]_3 chr2L:3600994-3601114 4.3e-05 68_[+5]_44 chr3R:26017442-26017562 4.3e-05 27_[+5]_85 chr3R:5016521-5016641 4.3e-05 11_[+5]_101 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TGYTGTTG MEME-5 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF TGYTGTTG width=8 seqs=13 chrX:21242013-21242133 ( 19) TGCTGTTG 1 chr3L:8395779-8395899 ( 103) TGCTGTTG 1 chr3R:26006025-26006145 ( 101) TGCTGTTG 1 chr2R:12019235-12019355 ( 16) TGTTGTTG 1 chr3R:22596542-22596662 ( 108) TGTTGTTG 1 chrX:22837503-22837623 ( 70) TGTTGTTG 1 chr2L:13082261-13082381 ( 13) TGTTGTTG 1 chr2R:17458407-17458527 ( 79) TGTTGTTG 1 chrX:19308111-19308231 ( 51) TGTTGTTG 1 chr3R:28845155-28845275 ( 110) TGTTGTTG 1 chr2L:3600994-3601114 ( 69) TGCTGCTG 1 chr3R:26017442-26017562 ( 28) TGCTGCTG 1 chr3R:5016521-5016641 ( 12) TGCTGCTG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TGYTGTTG MEME-5 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 28250 bayes= 11.6156 E= 1.1e+005 -1035 -1035 -1035 185 -1035 -1035 217 -1035 -1035 105 -1035 96 -1035 -1035 -1035 185 -1035 -1035 217 -1035 -1035 5 -1035 147 -1035 -1035 -1035 185 -1035 -1035 217 -1035 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TGYTGTTG MEME-5 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 13 E= 1.1e+005 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.461538 0.000000 0.538462 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.230769 0.000000 0.769231 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TGYTGTTG MEME-5 regular expression -------------------------------------------------------------------------------- TG[TC]TG[TC]TG -------------------------------------------------------------------------------- Time 32.18 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr3R:16338529-16338649 3.06e-02 39_[+1(2.21e-05)]_73 chr3R:24589104-24589224 6.65e-01 120 chr3R:29255231-29255351 2.10e-01 120 chr3L:15336626-15336746 5.23e-02 60_[+3(1.64e-05)]_52 chr3R:24057292-24057412 2.86e-01 120 chr3R:18122007-18122127 4.19e-01 120 chr2R:12780457-12780577 6.12e-01 120 chr3L:4227281-4227401 2.99e-01 120 chr2R:12174240-12174360 5.50e-01 120 chr2R:22136914-22137034 4.79e-04 5_[+4(1.65e-05)]_48_[+1(4.97e-05)]_\ 51 chr2L:20148518-20148638 1.45e-01 120 chrX:8271352-8271472 5.94e-03 84_[+1(9.51e-05)]_28 chr3R:26010923-26011043 8.71e-01 120 chrX:19153326-19153446 6.23e-01 120 chr2R:23567340-23567460 1.84e-04 14_[+1(2.21e-05)]_13_[+2(6.30e-05)]_\ 60_[+5(8.91e-05)]_9 chrX:6279214-6279334 9.11e-02 120 chr3L:1463776-1463896 1.70e-03 16_[+2(7.33e-06)]_33_[+4(2.38e-05)]_\ 55 chr2L:20104595-20104715 4.78e-01 120 chr3R:28845155-28845275 1.38e-01 109_[+5(3.18e-05)]_3 chr3L:11286698-11286818 4.46e-01 120 chr3L:18398374-18398494 1.32e-01 120 chr2R:20313573-20313693 2.37e-01 120 chr3R:9054334-9054454 9.08e-02 120 chrX:11137043-11137163 4.77e-02 120 chr2L:5944658-5944778 1.81e-01 120 chr2R:8242646-8242766 7.44e-02 120 chr2R:6494393-6494513 1.17e-02 6_[+2(7.33e-06)]_106 chr3R:5016521-5016641 4.26e-02 11_[+5(4.32e-05)]_101 chr3R:9057111-9057231 3.46e-02 120 chrX:10745337-10745457 9.04e-01 120 chr3R:22133803-22133923 9.40e-02 120 chr2R:20562339-20562459 1.94e-02 102_[+1(4.97e-05)]_10 chrX:17357643-17357763 9.20e-01 120 chr3L:22407034-22407154 1.86e-02 120 chr3R:26017442-26017562 5.69e-04 27_[+5(4.32e-05)]_75_[+2(7.33e-06)]_\ 2 chr2R:6938661-6938781 9.62e-01 120 chr3R:21660598-21660718 2.79e-01 120 chr3L:17530866-17530986 1.49e-04 68_[+2(8.78e-05)]_8_[+4(7.29e-06)]_\ 28 chr3R:20635722-20635842 3.87e-01 120 chr3R:12369215-12369335 9.90e-03 82_[+2(7.33e-06)]_30 chr3R:31059885-31060005 1.41e-01 120 chrX:19308111-19308231 5.50e-03 15_[+1(4.97e-05)]_27_[+5(3.18e-05)]_\ 62 chr2L:2753211-2753331 1.76e-04 5_[+2(7.04e-05)]_34_[+3(7.26e-06)]_\ 65 chr3R:13813009-13813129 5.74e-02 39_[+2(2.39e-05)]_73 chr2L:3675936-3676056 7.74e-01 120 chr2R:11175506-11175626 4.96e-01 120 chr2L:5906963-5907083 1.73e-01 120 chr3R:23445385-23445505 3.66e-01 120 chr3R:29265210-29265330 9.89e-01 120 chr2L:6725937-6726057 1.03e-04 7_[+4(7.29e-06)]_89_[+2(1.65e-05)]_\ 8 chr2R:17458407-17458527 1.64e-02 78_[+5(3.18e-05)]_34 chr2L:10238242-10238362 8.34e-01 120 chr2R:7663864-7663984 6.51e-01 120 chrX:8924980-8925100 1.13e-01 89_[+2(2.98e-05)]_23 chr3L:7858387-7858507 3.69e-01 120 chr2L:15333826-15333946 1.00e+00 120 chr2L:7544553-7544673 8.88e-01 120 chrX:3024668-3024788 1.07e-01 68_[+1(9.51e-05)]_44 chr3R:6818715-6818835 6.87e-01 120 chr3L:16711986-16712106 2.58e-01 120 chr2L:18987056-18987176 8.18e-02 120 chr4:980250-980370 4.70e-01 120 chr3R:8813728-8813848 3.32e-03 4_[+1(2.21e-05)]_108 chr2R:12034174-12034294 1.97e-01 3_[+2(5.55e-05)]_109 chrX:7098038-7098158 3.57e-01 120 chr3R:28634765-28634885 6.78e-02 120 chr2R:7885923-7886043 3.23e-02 120 chr3L:623736-623856 6.96e-01 120 chr3L:9505160-9505280 8.86e-01 120 chr3L:8347466-8347586 5.21e-03 87_[+2(1.65e-05)]_25 chr2R:18232748-18232868 2.25e-02 39_[+4(7.29e-06)]_73 chrX:13755333-13755453 1.12e-01 120 chr3R:19094165-19094285 2.72e-03 77_[+1(4.97e-05)]_35 chr2L:6956882-6957002 5.16e-01 120 chr3R:21856219-21856339 4.95e-01 120 chr2L:10221071-10221191 8.83e-01 120 chr3R:29841625-29841745 1.89e-01 120 chr2R:12025111-12025231 6.86e-03 68_[+4(1.65e-05)]_44 chrX:14211385-14211505 1.01e-01 120 chr3R:32051844-32051964 2.89e-03 79_[+3(1.64e-05)]_33 chr2R:17097357-17097477 6.73e-01 120 chr2L:6700797-6700917 1.40e-01 47_[+1(6.75e-05)]_65 chrX:17298021-17298141 6.94e-01 120 chr3R:5264931-5265051 8.71e-02 120 chr2L:19059047-19059167 9.98e-01 120 chr3R:21850345-21850465 4.48e-02 120 chr3R:11567032-11567152 2.35e-04 34_[+2(7.33e-06)]_13_[+3(1.64e-05)]_\ 57 chrX:10602417-10602537 1.17e-03 106_[+3(3.28e-05)]_6 chr2R:21475030-21475150 9.78e-01 120 chr2R:10238183-10238303 5.65e-01 120 chr3L:11429674-11429794 9.26e-01 120 chr3R:11372821-11372941 6.94e-01 120 chr3L:15142527-15142647 7.34e-01 120 chr3L:224232-224352 7.70e-01 120 chr2L:7306953-7307073 2.88e-01 120 chr2R:13008241-13008361 3.30e-01 7_[+2(5.55e-05)]_105 chr3R:19164919-19165039 2.34e-01 120 chr2L:8554337-8554457 4.38e-01 120 chr2L:901397-901517 5.42e-02 120 chr2R:12274381-12274501 9.15e-03 90_[+1(2.21e-05)]_22 chr2L:13838759-13838879 1.18e-01 80_[+1(6.75e-05)]_1_[+1(2.21e-05)]_\ 23 chr2L:3600994-3601114 1.80e-01 68_[+5(4.32e-05)]_44 chr2R:23551107-23551227 9.23e-01 120 chr2L:4892102-4892222 7.47e-01 120 chr3L:16760354-16760474 9.72e-01 120 chr2L:13203956-13204076 3.88e-01 120 chr2R:19451516-19451636 4.73e-01 120 chr2R:24965079-24965199 1.98e-01 120 chr2L:7998835-7998955 8.49e-01 120 chr2L:901609-901729 6.49e-01 120 chr2L:13082261-13082381 1.14e-02 12_[+5(3.18e-05)]_33_[+1(9.51e-05)]_\ 59 chr2L:16816070-16816190 6.92e-01 120 chr2R:12259376-12259496 1.62e-02 53_[+3(1.64e-05)]_59 chr3R:10598169-10598289 8.58e-01 120 chrX:22837503-22837623 1.83e-02 69_[+5(3.18e-05)]_43 chrX:13128081-13128201 1.12e-01 3_[+1(9.51e-05)]_109 chr3L:10845291-10845411 9.04e-01 120 chr3R:22041813-22041933 1.65e-03 4_[+1(6.75e-05)]_108 chrX:13404005-13404125 9.11e-01 120 chr2L:11417657-11417777 9.94e-01 120 chr2R:13482152-13482272 2.91e-01 87_[+1(4.97e-05)]_25 chr3R:16431761-16431881 2.15e-01 120 chr3L:19000629-19000749 6.17e-01 120 chr3R:26006025-26006145 1.89e-05 [+2(5.55e-05)]_54_[+4(7.29e-06)]_30_\ [+5(1.42e-05)]_12 chr3R:23943017-23943137 4.31e-01 120 chr2L:7339766-7339886 6.43e-02 15_[+1(2.21e-05)]_97 chrX:11548787-11548907 9.99e-01 120 chr3R:21377327-21377447 1.70e-01 120 chr3R:31395292-31395412 1.77e-01 120 chr3L:7359970-7360090 6.86e-03 14_[+3(7.26e-06)]_98 chr3R:20276148-20276268 2.98e-01 120 chr2R:8615278-8615398 3.61e-01 120 chr3R:18242731-18242851 4.75e-01 120 chr3L:16770015-16770135 8.90e-02 108_[+2(5.55e-05)]_4 chr2R:15735253-15735373 4.64e-01 120 chrX:3357741-3357861 4.63e-01 120 chr3R:20263915-20264035 4.91e-01 120 chr2L:14376964-14377084 9.83e-01 120 chr3R:8819679-8819799 3.01e-02 82_[+1(2.21e-05)]_30 chr3R:22147627-22147747 6.79e-01 120 chr2L:19159564-19159684 1.15e-01 96_[+2(9.69e-05)]_16 chrX:15498984-15499104 7.18e-02 107_[+3(7.26e-06)]_5 chrX:18774960-18775080 3.80e-02 18_[+1(9.51e-05)]_94 chr3R:13051370-13051490 3.06e-02 120 chr3L:14190842-14190962 4.58e-01 120 chr3R:9055255-9055375 6.47e-02 120 chrX:3367386-3367506 6.95e-01 120 chr3L:14131772-14131892 1.97e-02 58_[+4(1.65e-05)]_54 chr3L:129414-129534 7.09e-01 120 chr2L:10967411-10967531 2.50e-01 120 chr2L:11037957-11038077 5.50e-01 120 chr3L:8584236-8584356 9.74e-01 120 chr2L:7043210-7043330 2.81e-04 3_[+2(1.65e-05)]_10_[+1(2.21e-05)]_\ 91 chr3R:20948106-20948226 7.39e-01 120 chr2L:8573060-8573180 6.19e-01 120 chr3R:30428004-30428124 5.40e-01 120 chrX:18635404-18635524 8.16e-01 120 chrX:4106076-4106196 6.01e-01 120 chr2R:8649510-8649630 2.10e-03 30_[+2(3.72e-05)]_82 chr2R:11541272-11541392 9.43e-01 120 chr2R:18802358-18802478 1.76e-01 120 chr2L:18666052-18666172 1.12e-01 120 chr3R:7977709-7977829 3.94e-01 120 chr3L:5987778-5987898 1.53e-02 88_[+1(4.97e-05)]_24 chr2R:11095296-11095416 8.53e-01 120 chr3R:17053974-17054094 4.52e-01 120 chr2L:18822968-18823088 5.65e-01 120 chr2L:10516519-10516639 2.96e-02 9_[+2(6.30e-05)]_103 chr3R:19472342-19472462 9.85e-01 120 chr3L:6059194-6059314 1.36e-03 24_[+3(7.26e-06)]_88 chr3R:9344814-9344934 2.66e-03 34_[+2(5.55e-05)]_47_[+1(4.97e-05)]_\ 23 chr3R:6405826-6405946 2.05e-01 120 chr3L:1177157-1177277 1.06e-01 17_[+5(3.18e-05)]_16_[+5(3.18e-05)]_\ 71 chr3L:9028170-9028290 6.96e-01 120 chr3L:1795343-1795463 7.83e-01 120 chr2L:3477382-3477502 9.98e-01 120 chr3R:16235618-16235738 2.79e-02 120 chrX:8650853-8650973 2.49e-01 120 chr2L:1428412-1428532 9.84e-01 120 chrX:15076139-15076259 2.77e-03 120 chrX:10582169-10582289 1.44e-01 120 chr3L:21536951-21537071 9.95e-01 120 chr3L:7356406-7356526 9.23e-03 69_[+1(4.97e-05)]_43 chr2R:24028507-24028627 9.66e-01 120 chr2L:20950864-20950984 5.81e-01 120 chr3R:8233504-8233624 8.83e-01 120 chr3R:18366425-18366545 6.53e-01 120 chr3R:23314507-23314627 5.84e-01 120 chr3L:14555055-14555175 6.08e-02 32_[+2(7.33e-06)]_80 chr4:446064-446184 4.73e-01 120 chr3L:14786256-14786376 2.66e-03 23_[+2(5.55e-05)]_89 chr3R:29556262-29556382 6.64e-02 120 chr3L:14195830-14195950 1.25e-01 120 chr2R:23940165-23940285 9.42e-01 120 chr3L:8395779-8395899 3.29e-03 102_[+5(1.42e-05)]_10 chr2L:222254-222374 3.96e-02 120 chr3R:15794532-15794652 2.63e-01 120 chr3R:23333948-23334068 2.31e-01 120 chr2L:13205446-13205566 6.12e-02 12_[+2(8.78e-05)]_100 chr3L:642910-643030 1.13e-04 27_[+5(8.91e-05)]_11_[+1(2.21e-05)]_\ 66 chr2R:17719360-17719480 3.22e-01 120 chr3R:17584125-17584245 1.00e+00 120 chr3L:21007859-21007979 4.04e-01 120 chr2R:11639674-11639794 7.66e-01 120 chr2R:24174592-24174712 9.90e-01 120 chr3L:5857084-5857204 9.82e-01 120 chr2L:20945334-20945454 9.55e-01 120 chr3L:813414-813534 8.21e-01 120 chrX:19770322-19770442 6.64e-01 120 chr3R:21065216-21065336 4.64e-01 120 chr3L:15715895-15716015 1.62e-01 120 chr2L:13215960-13216080 8.09e-01 120 chr3L:15728315-15728435 3.80e-03 120 chr3R:21270105-21270225 2.20e-02 70_[+1(4.97e-05)]_42 chr2L:21370854-21370974 1.90e-01 93_[+2(3.72e-05)]_19 chr3L:1295782-1295902 8.22e-01 120 chr2R:18514006-18514126 2.46e-01 120 chr2L:3566701-3566821 9.98e-01 120 chr3L:18114483-18114603 2.86e-01 120 chr3R:27273558-27273678 9.46e-01 120 chr3L:2466754-2466874 8.82e-01 120 chr3L:11534139-11534259 7.61e-02 109_[+1(4.97e-05)]_3 chr2R:10096806-10096926 6.99e-01 120 chrX:9137320-9137440 7.56e-01 120 chr3L:14956430-14956550 6.65e-01 120 chr3R:11569069-11569189 9.54e-01 120 chr3L:11205889-11206009 3.64e-01 31_[+1(9.51e-05)]_81 chr3R:15676356-15676476 2.30e-02 76_[+1(2.21e-05)]_36 chr2L:14545433-14545553 8.36e-01 120 chr3L:19575812-19575932 8.19e-01 120 chr2R:18662407-18662527 7.34e-01 120 chr3R:22596542-22596662 7.50e-04 107_[+5(3.18e-05)]_5 chr2R:18242057-18242177 5.76e-01 120 chrX:7333331-7333451 3.94e-01 120 chr3R:12718315-12718435 4.47e-01 120 chr2R:12878809-12878929 6.38e-01 120 chr2L:10339470-10339590 8.03e-03 35_[+2(5.55e-05)]_77 chr3R:20830373-20830493 6.96e-03 120 chr3R:16186828-16186948 7.18e-01 120 chr2R:12019235-12019355 4.36e-02 15_[+5(3.18e-05)]_97 chr2R:12605671-12605791 7.67e-01 120 chr3R:9870126-9870246 8.63e-02 120 chr3R:5613134-5613254 7.53e-01 120 chr3L:4138957-4139077 2.10e-01 120 chr3L:3767949-3768069 8.18e-02 120 chr2L:21237130-21237250 3.81e-01 120 chr3L:6264562-6264682 3.56e-01 120 chrX:21242013-21242133 5.02e-04 10_[+1(2.21e-05)]_[+5(1.42e-05)]_42_\ [+1(2.21e-05)]_8_[+1(2.21e-05)]_28 chr2R:8144784-8144904 7.08e-01 120 chr3R:26654738-26654858 6.57e-02 120 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (5) found. ******************************************************************************** CPU: c27n09.farnam.hpc.yale.internal ********************************************************************************