******************************************************************************** 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/CG18599.fasta CONTROL SEQUENCES= --none-- ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ chr2R:20797083-20797203 1.0000 120 chr2L:14887622-14887742 1.0000 120 chr2R:22787529-22787649 1.0000 120 chrX:11295515-11295635 1.0000 120 chr3L:20062695-20062815 1.0000 120 chrX:9431534-9431654 1.0000 120 chr3R:26182144-26182264 1.0000 120 chr2R:18686963-18687083 1.0000 120 chr2L:16921972-16922092 1.0000 120 chrX:13023914-13024034 1.0000 120 chrX:5847638-5847758 1.0000 120 chr3R:28020732-28020852 1.0000 120 chr3R:17371201-17371321 1.0000 120 chr3R:23612239-23612359 1.0000 120 chr3R:25854942-25855062 1.0000 120 chr3R:24474918-24475038 1.0000 120 chr2L:11902634-11902754 1.0000 120 chr3R:13575418-13575538 1.0000 120 chr3L:3801483-3801603 1.0000 120 chr3R:27613967-27614087 1.0000 120 chr3L:1011104-1011224 1.0000 120 chr3R:7334794-7334914 1.0000 120 chr3R:31949581-31949701 1.0000 120 chr3R:24091733-24091853 1.0000 120 chr2R:14726112-14726232 1.0000 120 chr3R:14912704-14912824 1.0000 120 chr3L:5297357-5297477 1.0000 120 chr3L:10033437-10033557 1.0000 120 chr3R:27662132-27662252 1.0000 120 chr3L:10482663-10482783 1.0000 120 chr2R:22787728-22787848 1.0000 120 chr3R:30550150-30550270 1.0000 120 chr2L:17159810-17159930 1.0000 120 chr3R:29978741-29978861 1.0000 120 chr2R:18480475-18480595 1.0000 120 chr2R:9756279-9756399 1.0000 120 chr3R:15119855-15119975 1.0000 120 chr3R:7687007-7687127 1.0000 120 chr2R:17918907-17919027 1.0000 120 chr2L:1828419-1828539 1.0000 120 chr2R:12203280-12203400 1.0000 120 chr3R:25968638-25968758 1.0000 120 chrX:1706057-1706177 1.0000 120 chr3R:25152426-25152546 1.0000 120 chrX:6439607-6439727 1.0000 120 chrX:15304385-15304505 1.0000 120 chrX:20797647-20797767 1.0000 120 chrX:6152063-6152183 1.0000 120 chr3R:24467393-24467513 1.0000 120 chr2R:23819957-23820077 1.0000 120 chr2R:7765171-7765291 1.0000 120 chr3R:29651632-29651752 1.0000 120 chr2L:15179136-15179256 1.0000 120 chr3R:16168250-16168370 1.0000 120 chr3L:3479691-3479811 1.0000 120 chrX:10250818-10250938 1.0000 120 chr3R:13091831-13091951 1.0000 120 chr3L:20848731-20848851 1.0000 120 chr2L:13049270-13049390 1.0000 120 chr3R:17237082-17237202 1.0000 120 chrX:9520354-9520474 1.0000 120 chr3R:14348565-14348685 1.0000 120 chr2L:4248425-4248545 1.0000 120 chr2R:12739839-12739959 1.0000 120 chr3R:12751140-12751260 1.0000 120 chr2R:16916277-16916397 1.0000 120 chr2R:23154679-23154799 1.0000 120 chrX:12870036-12870156 1.0000 120 chr2L:2501978-2502098 1.0000 120 chr3L:11863722-11863842 1.0000 120 chr3R:8546068-8546188 1.0000 120 chr3R:28297636-28297756 1.0000 120 chr3R:22822847-22822967 1.0000 120 chr2R:13098830-13098950 1.0000 120 chr3L:10599642-10599762 1.0000 120 chr2L:2350198-2350318 1.0000 120 chr3L:12874315-12874435 1.0000 120 chr3L:10496398-10496518 1.0000 120 chrX:966957-967077 1.0000 120 chr3R:12591843-12591963 1.0000 120 chrX:5143988-5144108 1.0000 120 chr2R:16770382-16770502 1.0000 120 chr2L:3939000-3939120 1.0000 120 chr3R:28118236-28118356 1.0000 120 chr3R:20719394-20719514 1.0000 120 chr3R:22503748-22503868 1.0000 120 chr2L:6310055-6310175 1.0000 120 chr3L:11402413-11402533 1.0000 120 chr3R:17178289-17178409 1.0000 120 chr2L:18267940-18268060 1.0000 120 chr3L:17671909-17672029 1.0000 120 chr2L:2314302-2314422 1.0000 120 chr3R:29075788-29075908 1.0000 120 chr2L:17207263-17207383 1.0000 120 chr2R:17156231-17156351 1.0000 120 chr2L:9864493-9864613 1.0000 120 chr3L:13986475-13986595 1.0000 120 chr3R:10726867-10726987 1.0000 120 chr3R:8577711-8577831 1.0000 120 chr2L:1043736-1043856 1.0000 120 chr3R:26671820-26671940 1.0000 120 chr3R:30560680-30560800 1.0000 120 chrX:524494-524614 1.0000 120 chr2L:4146439-4146559 1.0000 120 chr2R:22976631-22976751 1.0000 120 chr3R:18508379-18508499 1.0000 120 chr3R:29625990-29626110 1.0000 120 chr3R:18279744-18279864 1.0000 120 chr3R:21809065-21809185 1.0000 120 chr3L:2332368-2332488 1.0000 120 chr3L:17448082-17448202 1.0000 120 chr2L:7675454-7675574 1.0000 120 chr3L:2913421-2913541 1.0000 120 chr3R:8072777-8072897 1.0000 120 chr3L:2410962-2411082 1.0000 120 chr2R:19971489-19971609 1.0000 120 chr2R:22789410-22789530 1.0000 120 chr3R:11024877-11024997 1.0000 120 chr2R:10400120-10400240 1.0000 120 chr2L:9400327-9400447 1.0000 120 chr3R:26333411-26333531 1.0000 120 chr2R:13723377-13723497 1.0000 120 chr2L:413132-413252 1.0000 120 chrX:5409005-5409125 1.0000 120 chr3L:17310611-17310731 1.0000 120 chrX:18468005-18468125 1.0000 120 chr2L:2348644-2348764 1.0000 120 chrX:9004498-9004618 1.0000 120 chrX:13676584-13676704 1.0000 120 chrX:18125719-18125839 1.0000 120 chrX:4691326-4691446 1.0000 120 chr2L:3755274-3755394 1.0000 120 chr3R:30325588-30325708 1.0000 120 chrX:3273680-3273800 1.0000 120 chr2L:18186834-18186954 1.0000 120 chr2R:15515768-15515888 1.0000 120 chrX:7550883-7551003 1.0000 120 chr3R:15898500-15898620 1.0000 120 chr3R:24073883-24074003 1.0000 120 chrX:12073771-12073891 1.0000 120 chrX:4005202-4005322 1.0000 120 chr2R:24629556-24629676 1.0000 120 chrX:10757768-10757888 1.0000 120 chr3R:31630501-31630621 1.0000 120 chr3R:22108476-22108596 1.0000 120 chr2L:14141361-14141481 1.0000 120 chr2L:4861634-4861754 1.0000 120 chr3R:26494404-26494524 1.0000 120 chr3L:15923433-15923553 1.0000 120 chr2L:16716972-16717092 1.0000 120 chrX:19818712-19818832 1.0000 120 chr3R:17526219-17526339 1.0000 120 chr3L:19340642-19340762 1.0000 120 chr3R:12543042-12543162 1.0000 120 chrX:17021616-17021736 1.0000 120 chrX:2861101-2861221 1.0000 120 chr3L:19961919-19962039 1.0000 120 chr3R:28959295-28959415 1.0000 120 chr3L:19845670-19845790 1.0000 120 chrX:4762443-4762563 1.0000 120 chr2L:1135642-1135762 1.0000 120 chr3L:1976868-1976988 1.0000 120 chrX:19453308-19453428 1.0000 120 chrX:7995191-7995311 1.0000 120 chr2L:6868692-6868812 1.0000 120 chr2R:16911851-16911971 1.0000 120 chrX:5095705-5095825 1.0000 120 chr2L:20808396-20808516 1.0000 120 chr2R:7139390-7139510 1.0000 120 chr3L:8094641-8094761 1.0000 120 chr2L:2528210-2528330 1.0000 120 chr3L:19969315-19969435 1.0000 120 chr3R:14279733-14279853 1.0000 120 chr2L:892590-892710 1.0000 120 chr3L:21859830-21859950 1.0000 120 chr3R:31424582-31424702 1.0000 120 chr3L:4010217-4010337 1.0000 120 chr2R:21895014-21895134 1.0000 120 chr2L:20951462-20951582 1.0000 120 chr3R:28429725-28429845 1.0000 120 chr2R:16778142-16778262 1.0000 120 chr2R:17206037-17206157 1.0000 120 chr2R:11144974-11145094 1.0000 120 chr2L:11628415-11628535 1.0000 120 chr3R:9938621-9938741 1.0000 120 chr2L:4928476-4928596 1.0000 120 chr3L:882427-882547 1.0000 120 chr3R:26280483-26280603 1.0000 120 chr3R:31636669-31636789 1.0000 120 chrX:13208113-13208233 1.0000 120 chr2L:1214609-1214729 1.0000 120 chr3L:17791657-17791777 1.0000 120 chr3R:16476586-16476706 1.0000 120 chrX:948320-948440 1.0000 120 chr2R:15155165-15155285 1.0000 120 chr3L:17458969-17459089 1.0000 120 chrX:7488374-7488494 1.0000 120 chr3L:19231345-19231465 1.0000 120 chrX:22488377-22488497 1.0000 120 chr3L:18837983-18838103 1.0000 120 chr3R:10024180-10024300 1.0000 120 chr2L:5569650-5569770 1.0000 120 chr3R:23110941-23111061 1.0000 120 chr3R:29111897-29112017 1.0000 120 chrX:8830281-8830401 1.0000 120 chr2R:24292870-24292990 1.0000 120 chr2L:1619317-1619437 1.0000 120 chr3L:2894830-2894950 1.0000 120 chrX:14727706-14727826 1.0000 120 chr3R:30489924-30490044 1.0000 120 chr2L:937081-937201 1.0000 120 chrX:10184798-10184918 1.0000 120 chrX:20434669-20434789 1.0000 120 chr2L:1316562-1316682 1.0000 120 chr3L:3411900-3412020 1.0000 120 chrX:13208314-13208434 1.0000 120 chr3L:1139529-1139649 1.0000 120 chr2R:15073194-15073314 1.0000 120 chr2R:23656700-23656820 1.0000 120 chr2L:4292689-4292809 1.0000 120 chr3L:13903372-13903492 1.0000 120 chr3R:30198950-30199070 1.0000 120 chr3L:15034374-15034494 1.0000 120 chr3L:19087932-19088052 1.0000 120 chr2L:1837841-1837961 1.0000 120 chrX:2161093-2161213 1.0000 120 chr2L:18966965-18967085 1.0000 120 chr2L:19285592-19285712 1.0000 120 chr3R:7821710-7821830 1.0000 120 chr2L:13461111-13461231 1.0000 120 chr2R:10013328-10013448 1.0000 120 chr2L:19930237-19930357 1.0000 120 chr3R:19622075-19622195 1.0000 120 chr3L:5280083-5280203 1.0000 120 chr3R:18296247-18296367 1.0000 120 chr2R:24139214-24139334 1.0000 120 chr2R:7749769-7749889 1.0000 120 chr3R:22719626-22719746 1.0000 120 chrX:13817591-13817711 1.0000 120 chr3L:5182402-5182522 1.0000 120 chr2L:17558267-17558387 1.0000 120 chrX:18004304-18004424 1.0000 120 chrX:2199492-2199612 1.0000 120 chr3L:13912903-13913023 1.0000 120 chrX:12937999-12938119 1.0000 120 chr3R:5302176-5302296 1.0000 120 chrX:18494304-18494424 1.0000 120 chr3R:12657118-12657238 1.0000 120 chr3R:26859328-26859448 1.0000 120 chr2L:11203751-11203871 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_CG18599/ -dna -nmotifs 5 -w 8 -maxsize 250000 -nostatus ../result/final_prediction/fly/fasta/RankLinear8.0_60/CG18599.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 0.343 C 0.156 G 0.156 T 0.344 Background letter frequencies (from file dataset with add-one prior applied): A 0.343 C 0.156 G 0.156 T 0.344 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF YCAGTGCA MEME-1 width = 8 sites = 34 llr = 312 E-value = 3.1e-007 ******************************************************************************** -------------------------------------------------------------------------------- Motif YCAGTGCA MEME-1 Description -------------------------------------------------------------------------------- Simplified A 1:a::::7 pos.-specific C 38::::7: probability G :2:a:a:2 matrix T 6:::a:31 bits 2.7 * * 2.4 * * 2.1 * * 1.9 * * * Relative 1.6 ***** Entropy 1.3 ****** (13.2 bits) 1.1 ****** 0.8 ******** 0.5 ******** 0.3 ******** 0.0 -------- Multilevel TCAGTGCA consensus CG TG sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif YCAGTGCA MEME-1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chrX:4762443-4762563 73 3.74e-06 CTTACTTTTG CCAGTGCA CAAAACCCGC chrX:17021616-17021736 104 3.74e-06 CTCATTTTTT CCAGTGCA TGTCGTGGT chr3R:22108476-22108596 110 3.74e-06 GGTATTTTTT CCAGTGCA CAA chr2R:17156231-17156351 93 3.74e-06 CCGGCTTTTC CCAGTGCA TGCGAGAACG chr3R:28959295-28959415 112 1.20e-05 ATAATTTCTC TCAGTGCA T chr3R:22503748-22503868 67 1.20e-05 TGCTGCGTAC TCAGTGCA GTATATATGT chr3R:13091831-13091951 103 1.20e-05 GCAATTGTTT TCAGTGCA CTGGTGCTGC chr3R:7334794-7334914 104 1.20e-05 TTCATTTCGT TCAGTGCA CTTTCTAAG chrX:2199492-2199612 32 1.37e-05 GGCCAAGTGT CCAGTGCG TCGATACGCA chr2L:3939000-3939120 94 1.74e-05 ATTTGATAAA TCAGTGCG CCGAGTGACC chr2L:17159810-17159930 77 1.74e-05 TATTATTCTC TCAGTGCG TAGAGAAGCA chr3R:27662132-27662252 105 1.74e-05 TCCCGTCCAT TCAGTGCG TATACTTA chr3R:7687007-7687127 107 2.12e-05 ATCATTTTTC CGAGTGCA GGCAAA chr2L:19930237-19930357 111 2.94e-05 CGAGTTTCTT CCAGTGTA AG chr3R:31636669-31636789 105 2.94e-05 CCGATTTTGC CCAGTGTA ATCGCTGA chr3R:17237082-17237202 80 2.94e-05 CCATTTCTTC CCAGTGTA GATATAAAAT chr3R:29651632-29651752 41 2.94e-05 ACAGTACAAA CCAGTGTA AGCTAAAAAT chr2L:11203751-11203871 106 3.77e-05 TTTATTTCTC TGAGTGCA GGGTGCT chrX:2161093-2161213 73 3.77e-05 TCTCAAACTG TGAGTGCA TACTTTGACT chr2L:1837841-1837961 33 3.77e-05 TGCTTAAAAC TGAGTGCA ACTGAAATAA chr2R:11144974-11145094 105 3.77e-05 GCACTTTTTC TGAGTGCA CACAGCTG chr2L:20951462-20951582 94 3.77e-05 ACATTTTTTC TGAGTGCA CTGAGAAAAA chr2R:22976631-22976751 105 3.77e-05 CTAAAGTGAT TGAGTGCA AAGTATTT chr3L:5182402-5182522 110 5.58e-05 TGAATTTATT TCAGTGTA AGT chr3R:11024877-11024997 84 5.58e-05 TCCTTTTCTC TCAGTGTA GTGCCTTGTG chr2L:1828419-1828539 96 5.58e-05 TCACTTTCTC TCAGTGTA ATCCGCTGCG chr3R:27613967-27614087 112 5.58e-05 ATTTTTTTTA TCAGTGTA T chr3R:28429725-28429845 113 7.33e-05 GATTTTTCGC TCAGTGTG chr3L:20848731-20848851 83 7.33e-05 GCAAAGGTGA TCAGTGTG ACGCATAAGG chrX:20797647-20797767 113 7.33e-05 AGAACTTTTC TCAGTGTG chrX:18494304-18494424 113 8.53e-05 CTAGCACCTT ACAGTGCA chrX:19818712-19818832 29 8.53e-05 AAAACAACAA CCAGTGCT TGGACATCAA chr3R:28297636-28297756 50 8.53e-05 GGTTAGTATC ACAGTGCA ATAACGCTTA chr2L:2348644-2348764 110 9.36e-05 CTAGTTTTTT TCAGTGCT GCT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif YCAGTGCA MEME-1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrX:4762443-4762563 3.7e-06 72_[+1]_40 chrX:17021616-17021736 3.7e-06 103_[+1]_9 chr3R:22108476-22108596 3.7e-06 109_[+1]_3 chr2R:17156231-17156351 3.7e-06 92_[+1]_20 chr3R:28959295-28959415 1.2e-05 111_[+1]_1 chr3R:22503748-22503868 1.2e-05 66_[+1]_46 chr3R:13091831-13091951 1.2e-05 102_[+1]_10 chr3R:7334794-7334914 1.2e-05 103_[+1]_9 chrX:2199492-2199612 1.4e-05 31_[+1]_81 chr2L:3939000-3939120 1.7e-05 93_[+1]_19 chr2L:17159810-17159930 1.7e-05 76_[+1]_36 chr3R:27662132-27662252 1.7e-05 104_[+1]_8 chr3R:7687007-7687127 2.1e-05 106_[+1]_6 chr2L:19930237-19930357 2.9e-05 110_[+1]_2 chr3R:31636669-31636789 2.9e-05 104_[+1]_8 chr3R:17237082-17237202 2.9e-05 79_[+1]_33 chr3R:29651632-29651752 2.9e-05 40_[+1]_72 chr2L:11203751-11203871 3.8e-05 105_[+1]_7 chrX:2161093-2161213 3.8e-05 72_[+1]_40 chr2L:1837841-1837961 3.8e-05 32_[+1]_80 chr2R:11144974-11145094 3.8e-05 104_[+1]_8 chr2L:20951462-20951582 3.8e-05 93_[+1]_19 chr2R:22976631-22976751 3.8e-05 104_[+1]_8 chr3L:5182402-5182522 5.6e-05 109_[+1]_3 chr3R:11024877-11024997 5.6e-05 83_[+1]_29 chr2L:1828419-1828539 5.6e-05 95_[+1]_17 chr3R:27613967-27614087 5.6e-05 111_[+1]_1 chr3R:28429725-28429845 7.3e-05 112_[+1] chr3L:20848731-20848851 7.3e-05 82_[+1]_30 chrX:20797647-20797767 7.3e-05 112_[+1] chrX:18494304-18494424 8.5e-05 112_[+1] chrX:19818712-19818832 8.5e-05 28_[+1]_84 chr3R:28297636-28297756 8.5e-05 49_[+1]_63 chr2L:2348644-2348764 9.4e-05 109_[+1]_3 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif YCAGTGCA MEME-1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF YCAGTGCA width=8 seqs=34 chrX:4762443-4762563 ( 73) CCAGTGCA 1 chrX:17021616-17021736 ( 104) CCAGTGCA 1 chr3R:22108476-22108596 ( 110) CCAGTGCA 1 chr2R:17156231-17156351 ( 93) CCAGTGCA 1 chr3R:28959295-28959415 ( 112) TCAGTGCA 1 chr3R:22503748-22503868 ( 67) TCAGTGCA 1 chr3R:13091831-13091951 ( 103) TCAGTGCA 1 chr3R:7334794-7334914 ( 104) TCAGTGCA 1 chrX:2199492-2199612 ( 32) CCAGTGCG 1 chr2L:3939000-3939120 ( 94) TCAGTGCG 1 chr2L:17159810-17159930 ( 77) TCAGTGCG 1 chr3R:27662132-27662252 ( 105) TCAGTGCG 1 chr3R:7687007-7687127 ( 107) CGAGTGCA 1 chr2L:19930237-19930357 ( 111) CCAGTGTA 1 chr3R:31636669-31636789 ( 105) CCAGTGTA 1 chr3R:17237082-17237202 ( 80) CCAGTGTA 1 chr3R:29651632-29651752 ( 41) CCAGTGTA 1 chr2L:11203751-11203871 ( 106) TGAGTGCA 1 chrX:2161093-2161213 ( 73) TGAGTGCA 1 chr2L:1837841-1837961 ( 33) TGAGTGCA 1 chr2R:11144974-11145094 ( 105) TGAGTGCA 1 chr2L:20951462-20951582 ( 94) TGAGTGCA 1 chr2R:22976631-22976751 ( 105) TGAGTGCA 1 chr3L:5182402-5182522 ( 110) TCAGTGTA 1 chr3R:11024877-11024997 ( 84) TCAGTGTA 1 chr2L:1828419-1828539 ( 96) TCAGTGTA 1 chr3R:27613967-27614087 ( 112) TCAGTGTA 1 chr3R:28429725-28429845 ( 113) TCAGTGTG 1 chr3L:20848731-20848851 ( 83) TCAGTGTG 1 chrX:20797647-20797767 ( 113) TCAGTGTG 1 chrX:18494304-18494424 ( 113) ACAGTGCA 1 chrX:19818712-19818832 ( 29) CCAGTGCT 1 chr3R:28297636-28297756 ( 50) ACAGTGCA 1 chr2L:2348644-2348764 ( 110) TCAGTGCT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif YCAGTGCA MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 28250 bayes= 9.76639 E= 3.1e-007 -254 105 -1173 84 -1173 235 40 -1173 154 -1173 -1173 -1173 -1173 -1173 268 -1173 -1173 -1173 -1173 154 -1173 -1173 268 -1173 -1173 211 -1173 -9 110 -1173 40 -255 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif YCAGTGCA MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 34 E= 3.1e-007 0.058824 0.323529 0.000000 0.617647 0.000000 0.794118 0.205882 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.676471 0.000000 0.323529 0.735294 0.000000 0.205882 0.058824 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif YCAGTGCA MEME-1 regular expression -------------------------------------------------------------------------------- [TC][CG]AGTG[CT][AG] -------------------------------------------------------------------------------- Time 7.82 secs. ******************************************************************************** ******************************************************************************** MOTIF GCACTGAG MEME-2 width = 8 sites = 17 llr = 175 E-value = 7.6e-001 ******************************************************************************** -------------------------------------------------------------------------------- Motif GCACTGAG MEME-2 Description -------------------------------------------------------------------------------- Simplified A 2:a:1:63 pos.-specific C :a:a::3: probability G 8::::a17 matrix T ::::9::: bits 2.7 * * * 2.4 * * * 2.1 * * * 1.9 ** * * Relative 1.6 **** * Entropy 1.3 ****** * (14.9 bits) 1.1 ****** * 0.8 ******** 0.5 ******** 0.3 ******** 0.0 -------- Multilevel GCACTGAG consensus CA sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCACTGAG MEME-2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr3R:26859328-26859448 11 5.44e-06 AACGCAGTGT GCACTGAG AGAAAAGGAC chrX:2161093-2161213 5 5.44e-06 CGAC GCACTGCG AAAAAGTGCT chr2R:21895014-21895134 20 5.44e-06 CGGCTGGTAT GCACTGAG AGAAATAGTT chr2L:2528210-2528330 10 5.44e-06 AGACGAAAG GCACTGAG AGAAATTAGT chr2R:13098830-13098950 43 5.44e-06 TGTTACTTGT GCACTGAG AAAAACTTAG chr2L:15179136-15179256 5 5.44e-06 ATAT GCACTGCG GGAAAAATGT chr3R:17371201-17371321 7 5.44e-06 ATCCCT GCACTGAG AACAATCAAC chr3R:26280483-26280603 18 7.14e-06 TCAGTGGCAT GCACTGGG GAAAAAGGGG chr2L:937081-937201 47 1.91e-05 CTTGACTTGA GCACTGAA GAATTTGCTT chr3L:1976868-1976988 15 1.91e-05 GATGCTGGAT GCACTGAA AAAAAAACTA chrX:19818712-19818832 7 1.91e-05 ACTGAT GCACTGCA AAAAAAAACA chr3R:22822847-22822967 1 1.91e-05 . GCACTGAA AAAAACAAAA chr3R:25854942-25855062 13 1.91e-05 GCTAAATCCA GCACTGAA AAATTTTTCA chr2L:4292689-4292809 24 3.11e-05 ATGGAGAACT ACACTGAG CGCAAAATTA chr2L:4248425-4248545 5 3.11e-05 AAAT ACACTGCG AGAGATAAAG chrX:11295515-11295635 18 3.11e-05 CCTTTTCACC ACACTGAG GAAAATTATT chr3R:30489924-30490044 91 3.65e-05 ATCTTTGTTT GCACAGCG TTTATGTCTG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCACTGAG MEME-2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr3R:26859328-26859448 5.4e-06 10_[+2]_102 chrX:2161093-2161213 5.4e-06 4_[+2]_108 chr2R:21895014-21895134 5.4e-06 19_[+2]_93 chr2L:2528210-2528330 5.4e-06 9_[+2]_103 chr2R:13098830-13098950 5.4e-06 42_[+2]_70 chr2L:15179136-15179256 5.4e-06 4_[+2]_108 chr3R:17371201-17371321 5.4e-06 6_[+2]_106 chr3R:26280483-26280603 7.1e-06 17_[+2]_95 chr2L:937081-937201 1.9e-05 46_[+2]_66 chr3L:1976868-1976988 1.9e-05 14_[+2]_98 chrX:19818712-19818832 1.9e-05 6_[+2]_106 chr3R:22822847-22822967 1.9e-05 [+2]_112 chr3R:25854942-25855062 1.9e-05 12_[+2]_100 chr2L:4292689-4292809 3.1e-05 23_[+2]_89 chr2L:4248425-4248545 3.1e-05 4_[+2]_108 chrX:11295515-11295635 3.1e-05 17_[+2]_95 chr3R:30489924-30490044 3.6e-05 90_[+2]_22 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCACTGAG MEME-2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF GCACTGAG width=8 seqs=17 chr3R:26859328-26859448 ( 11) GCACTGAG 1 chrX:2161093-2161213 ( 5) GCACTGCG 1 chr2R:21895014-21895134 ( 20) GCACTGAG 1 chr2L:2528210-2528330 ( 10) GCACTGAG 1 chr2R:13098830-13098950 ( 43) GCACTGAG 1 chr2L:15179136-15179256 ( 5) GCACTGCG 1 chr3R:17371201-17371321 ( 7) GCACTGAG 1 chr3R:26280483-26280603 ( 18) GCACTGGG 1 chr2L:937081-937201 ( 47) GCACTGAA 1 chr3L:1976868-1976988 ( 15) GCACTGAA 1 chrX:19818712-19818832 ( 7) GCACTGCA 1 chr3R:22822847-22822967 ( 1) GCACTGAA 1 chr3R:25854942-25855062 ( 13) GCACTGAA 1 chr2L:4292689-4292809 ( 24) ACACTGAG 1 chr2L:4248425-4248545 ( 5) ACACTGCG 1 chrX:11295515-11295635 ( 18) ACACTGAG 1 chr3R:30489924-30490044 ( 91) GCACAGCG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCACTGAG MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 28250 bayes= 10.7672 E= 7.6e-001 -96 -1073 240 -1073 -1073 268 -1073 -1073 154 -1073 -1073 -1073 -1073 268 -1073 -1073 -254 -1073 -1073 145 -1073 -1073 268 -1073 91 91 -141 -1073 -22 -1073 218 -1073 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCACTGAG MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 17 E= 7.6e-001 0.176471 0.000000 0.823529 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 0.058824 0.000000 0.000000 0.941176 0.000000 0.000000 1.000000 0.000000 0.647059 0.294118 0.058824 0.000000 0.294118 0.000000 0.705882 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCACTGAG MEME-2 regular expression -------------------------------------------------------------------------------- GCACTG[AC][GA] -------------------------------------------------------------------------------- Time 14.25 secs. ******************************************************************************** ******************************************************************************** MOTIF CAGCTGTC MEME-3 width = 8 sites = 11 llr = 122 E-value = 2.1e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif CAGCTGTC MEME-3 Description -------------------------------------------------------------------------------- Simplified A :9:::::: pos.-specific C a1:a:::8 probability G ::a:2a32 matrix T ::::8:7: bits 2.7 * ** * 2.4 * ** * 2.1 * ** * 1.9 * ** * * Relative 1.6 * ** * * Entropy 1.3 * ** * * (16.0 bits) 1.1 ******** 0.8 ******** 0.5 ******** 0.3 ******** 0.0 -------- Multilevel CAGCTGTC consensus G sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CAGCTGTC MEME-3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr3L:18837983-18838103 53 3.75e-06 GGCTCAGAAG CAGCTGTC AAATGTAAAT chr3L:19340642-19340762 38 3.75e-06 ACTATTTACA CAGCTGTC TGTATTATAT chrX:3273680-3273800 83 3.75e-06 GGAATATTGA CAGCTGTC GGTCGATCGA chr3L:2894830-2894950 109 5.45e-06 CGTCGGCCAT CAGCTGGC CGCA chrX:5409005-5409125 88 5.45e-06 AACAATAACT CAGCTGGC CGAGTGGGCG chr3L:13986475-13986595 34 5.45e-06 AACATCTACA CAGCTGGC CCAAAGTAAA chr2R:23656700-23656820 35 7.15e-06 ATACATTAAT CAGCGGTC AAGTAACTAA chr3L:4010217-4010337 102 7.15e-06 CACCGAAAGC CAGCGGTC TAAATCCCTA chr3R:12657118-12657238 43 1.34e-05 AATGCCAAAT CAGCTGTG TCAACTGGAT chr3L:19845670-19845790 64 1.34e-05 AATTCACCTA CAGCTGTG GAATATGTTT chr3R:31949581-31949701 66 1.34e-05 TATACGAACT CCGCTGTC TAATAATAAC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CAGCTGTC MEME-3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr3L:18837983-18838103 3.8e-06 52_[+3]_60 chr3L:19340642-19340762 3.8e-06 37_[+3]_75 chrX:3273680-3273800 3.8e-06 82_[+3]_30 chr3L:2894830-2894950 5.5e-06 108_[+3]_4 chrX:5409005-5409125 5.5e-06 87_[+3]_25 chr3L:13986475-13986595 5.5e-06 33_[+3]_79 chr2R:23656700-23656820 7.2e-06 34_[+3]_78 chr3L:4010217-4010337 7.2e-06 101_[+3]_11 chr3R:12657118-12657238 1.3e-05 42_[+3]_70 chr3L:19845670-19845790 1.3e-05 63_[+3]_49 chr3R:31949581-31949701 1.3e-05 65_[+3]_47 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CAGCTGTC MEME-3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF CAGCTGTC width=8 seqs=11 chr3L:18837983-18838103 ( 53) CAGCTGTC 1 chr3L:19340642-19340762 ( 38) CAGCTGTC 1 chrX:3273680-3273800 ( 83) CAGCTGTC 1 chr3L:2894830-2894950 ( 109) CAGCTGGC 1 chrX:5409005-5409125 ( 88) CAGCTGGC 1 chr3L:13986475-13986595 ( 34) CAGCTGGC 1 chr2R:23656700-23656820 ( 35) CAGCGGTC 1 chr3L:4010217-4010337 ( 102) CAGCGGTC 1 chr3R:12657118-12657238 ( 43) CAGCTGTG 1 chr3L:19845670-19845790 ( 64) CAGCTGTG 1 chr3R:31949581-31949701 ( 66) CCGCTGTC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CAGCTGTC MEME-3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 28250 bayes= 10.8783 E= 2.1e+002 -1010 268 -1010 -1010 140 -78 -1010 -1010 -1010 -1010 268 -1010 -1010 268 -1010 -1010 -1010 -1010 22 125 -1010 -1010 268 -1010 -1010 -1010 81 108 -1010 239 22 -1010 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CAGCTGTC MEME-3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 11 E= 2.1e+002 0.000000 1.000000 0.000000 0.000000 0.909091 0.090909 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.181818 0.818182 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.272727 0.727273 0.000000 0.818182 0.181818 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CAGCTGTC MEME-3 regular expression -------------------------------------------------------------------------------- CAGCTG[TG]C -------------------------------------------------------------------------------- Time 20.65 secs. ******************************************************************************** ******************************************************************************** MOTIF CGCTGYGT MEME-4 width = 8 sites = 24 llr = 221 E-value = 5.9e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif CGCTGYGT MEME-4 Description -------------------------------------------------------------------------------- Simplified A :::1:::: pos.-specific C 6:a314:2 probability G 2a::9:a: matrix T 2::6:6:8 bits 2.7 * 2.4 ** * 2.1 ** * * 1.9 ** * * Relative 1.6 ** * * Entropy 1.3 ** * * (13.3 bits) 1.1 *** * ** 0.8 *** **** 0.5 ******** 0.3 ******** 0.0 -------- Multilevel CGCTGTGT consensus T C C C sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CGCTGYGT MEME-4 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr3L:2410962-2411082 2 7.73e-07 A CGCCGCGT GGTACACCGC chr3L:13912903-13913023 107 4.18e-06 GCCTTATACG CGCCGTGT TCATTT chrX:2199492-2199612 64 4.18e-06 ATAATCTTAT CGCCGTGT GGGCTGTAAT chr3L:2894830-2894950 88 4.18e-06 CTTTTCGAAA CGCCGTGT ACTCGTCGGC chr2R:19971489-19971609 105 8.30e-06 AGCGAAGCTT CGCTGTGT CTTTCGCC chr3R:29651632-29651752 113 8.30e-06 CATAATTTTT CGCTGTGT chr2L:1828419-1828539 107 9.07e-06 CAGTGTAATC CGCTGCGC ACTTGG chrX:948320-948440 83 1.23e-05 GCCGACCCAG GGCCGCGT TTTGTTGACG chr3L:19340642-19340762 71 1.57e-05 TTTACCATCG CGCAGCGT TTTCTTCTCG chr3R:26182144-26182264 108 2.15e-05 ACTAATTTCT GGCTGTGT AGCAT chr3R:5302176-5302296 10 2.40e-05 CAAGTGCCT GGCTGCGC AGCTGAAAAA chr3R:26859328-26859448 3 3.15e-05 AA CGCAGTGT GCACTGAGAG chr3R:29111897-29112017 25 3.15e-05 ACTGGAAGTG TGCTGCGT GGGCAATAAA chrX:4005202-4005322 112 3.15e-05 AGGTATTTTT CGCAGTGT A chr3R:22503748-22503868 57 3.15e-05 GAGCTAAAAA TGCTGCGT ACTCAGTGCA chr3L:3479691-3479811 33 3.85e-05 ATTTCAATTA GGCTGTGC TTAGTGAACA chr2L:19285592-19285712 78 4.84e-05 ATTTATTTAA TGCTGTGT CTAAGCTTTT chrX:15304385-15304505 101 4.84e-05 ATCCAGTACC TGCTGTGT TCACTGTAGc chr3R:30560680-30560800 31 6.48e-05 TGTAGTGCCA CGCCCCGC AAACAAACAC chrX:5143988-5144108 104 6.48e-05 GCAATTTTTT CGCTCTGT GCATGCACA chr2R:14726112-14726232 111 6.48e-05 CGATTTCCAA TGCTGTGC GT chr2L:1043736-1043856 50 6.90e-05 GAAAGGAAGC CGCCGAGT CTGAAGTGGA chrX:22488377-22488497 5 7.84e-05 TGGG CGGTGCGT TGCGGTCTAC chr3L:17448082-17448202 77 1.03e-04 AAACTTTTCT CCCTGTGT ATCTCCGCCT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CGCTGYGT MEME-4 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr3L:2410962-2411082 7.7e-07 1_[+4]_111 chr3L:13912903-13913023 4.2e-06 106_[+4]_6 chrX:2199492-2199612 4.2e-06 63_[+4]_49 chr3L:2894830-2894950 4.2e-06 87_[+4]_25 chr2R:19971489-19971609 8.3e-06 104_[+4]_8 chr3R:29651632-29651752 8.3e-06 112_[+4] chr2L:1828419-1828539 9.1e-06 106_[+4]_6 chrX:948320-948440 1.2e-05 82_[+4]_30 chr3L:19340642-19340762 1.6e-05 70_[+4]_42 chr3R:26182144-26182264 2.2e-05 107_[+4]_5 chr3R:5302176-5302296 2.4e-05 9_[+4]_103 chr3R:26859328-26859448 3.2e-05 2_[+4]_110 chr3R:29111897-29112017 3.2e-05 24_[+4]_88 chrX:4005202-4005322 3.2e-05 111_[+4]_1 chr3R:22503748-22503868 3.2e-05 56_[+4]_56 chr3L:3479691-3479811 3.9e-05 32_[+4]_80 chr2L:19285592-19285712 4.8e-05 77_[+4]_35 chrX:15304385-15304505 4.8e-05 100_[+4]_12 chr3R:30560680-30560800 6.5e-05 30_[+4]_82 chrX:5143988-5144108 6.5e-05 103_[+4]_9 chr2R:14726112-14726232 6.5e-05 110_[+4]_2 chr2L:1043736-1043856 6.9e-05 49_[+4]_63 chrX:22488377-22488497 7.8e-05 4_[+4]_108 chr3L:17448082-17448202 0.0001 76_[+4]_36 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CGCTGYGT MEME-4 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF CGCTGYGT width=8 seqs=24 chr3L:2410962-2411082 ( 2) CGCCGCGT 1 chr3L:13912903-13913023 ( 107) CGCCGTGT 1 chrX:2199492-2199612 ( 64) CGCCGTGT 1 chr3L:2894830-2894950 ( 88) CGCCGTGT 1 chr2R:19971489-19971609 ( 105) CGCTGTGT 1 chr3R:29651632-29651752 ( 113) CGCTGTGT 1 chr2L:1828419-1828539 ( 107) CGCTGCGC 1 chrX:948320-948440 ( 83) GGCCGCGT 1 chr3L:19340642-19340762 ( 71) CGCAGCGT 1 chr3R:26182144-26182264 ( 108) GGCTGTGT 1 chr3R:5302176-5302296 ( 10) GGCTGCGC 1 chr3R:26859328-26859448 ( 3) CGCAGTGT 1 chr3R:29111897-29112017 ( 25) TGCTGCGT 1 chrX:4005202-4005322 ( 112) CGCAGTGT 1 chr3R:22503748-22503868 ( 57) TGCTGCGT 1 chr3L:3479691-3479811 ( 33) GGCTGTGC 1 chr2L:19285592-19285712 ( 78) TGCTGTGT 1 chrX:15304385-15304505 ( 101) TGCTGTGT 1 chr3R:30560680-30560800 ( 31) CGCCCCGC 1 chrX:5143988-5144108 ( 104) CGCTCTGT 1 chr2R:14726112-14726232 ( 111) TGCTGTGC 1 chr2L:1043736-1043856 ( 50) CGCCGAGT 1 chrX:22488377-22488497 ( 5) CGGTGCGT 1 chr3L:17448082-17448202 ( 77) CCCTGTGT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CGCTGYGT MEME-4 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 28250 bayes= 11.3 E= 5.9e+001 -1123 200 10 -73 -1123 -191 262 -1123 -1123 262 -190 -1123 -146 90 -1123 76 -1123 -91 255 -1123 -304 126 -1123 76 -1123 -1123 268 -1123 -1123 41 -1123 120 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CGCTGYGT MEME-4 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 24 E= 5.9e+001 0.000000 0.625000 0.166667 0.208333 0.000000 0.041667 0.958333 0.000000 0.000000 0.958333 0.041667 0.000000 0.125000 0.291667 0.000000 0.583333 0.000000 0.083333 0.916667 0.000000 0.041667 0.375000 0.000000 0.583333 0.000000 0.000000 1.000000 0.000000 0.000000 0.208333 0.000000 0.791667 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CGCTGYGT MEME-4 regular expression -------------------------------------------------------------------------------- [CT]GC[TC]G[TC]G[TC] -------------------------------------------------------------------------------- Time 27.03 secs. ******************************************************************************** ******************************************************************************** MOTIF GGGCGCGS MEME-5 width = 8 sites = 4 llr = 48 E-value = 8.8e+003 ******************************************************************************** -------------------------------------------------------------------------------- Motif GGGCGCGS MEME-5 Description -------------------------------------------------------------------------------- Simplified A :::::::: pos.-specific C ::3838:5 probability G aa8383a5 matrix T :::::::: bits 2.7 ** * 2.4 ** * 2.1 ** * 1.9 ******* Relative 1.6 ******** Entropy 1.3 ******** (17.2 bits) 1.1 ******** 0.8 ******** 0.5 ******** 0.3 ******** 0.0 -------- Multilevel GGGCGCGC consensus CGCG G sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGGCGCGS MEME-5 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr2R:22787529-22787649 4 7.01e-07 AAG GGGCGCGC ACACACACAC chrX:5409005-5409125 101 3.51e-06 CTGGCCGAGT GGGCGGGC AATTACGAAC chr2R:13723377-13723497 7 3.51e-06 CAGTCT GGGCCCGG CATATTGATT chr2L:4292689-4292809 4 7.72e-06 GGA GGCGGCGG ACATGGAGAA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGGCGCGS MEME-5 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr2R:22787529-22787649 7e-07 3_[+5]_109 chrX:5409005-5409125 3.5e-06 100_[+5]_12 chr2R:13723377-13723497 3.5e-06 6_[+5]_106 chr2L:4292689-4292809 7.7e-06 3_[+5]_109 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGGCGCGS MEME-5 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF GGGCGCGS width=8 seqs=4 chr2R:22787529-22787649 ( 4) GGGCGCGC 1 chrX:5409005-5409125 ( 101) GGGCGGGC 1 chr2R:13723377-13723497 ( 7) GGGCCCGG 1 chr2L:4292689-4292809 ( 4) GGCGGCGG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGGCGCGS MEME-5 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 28250 bayes= 13.5228 E= 8.8e+003 -865 -865 268 -865 -865 -865 268 -865 -865 68 226 -865 -865 226 68 -865 -865 68 226 -865 -865 226 68 -865 -865 -865 268 -865 -865 168 168 -865 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGGCGCGS MEME-5 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 4 E= 8.8e+003 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.250000 0.750000 0.000000 0.000000 0.750000 0.250000 0.000000 0.000000 0.250000 0.750000 0.000000 0.000000 0.750000 0.250000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.500000 0.500000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGGCGCGS MEME-5 regular expression -------------------------------------------------------------------------------- GG[GC][CG][GC][CG]G[CG] -------------------------------------------------------------------------------- Time 33.28 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr2R:20797083-20797203 9.42e-01 120 chr2L:14887622-14887742 5.96e-01 120 chr2R:22787529-22787649 8.51e-05 3_[+5(7.01e-07)]_109 chrX:11295515-11295635 1.80e-01 17_[+2(3.11e-05)]_95 chr3L:20062695-20062815 9.93e-01 120 chrX:9431534-9431654 1.43e-01 120 chr3R:26182144-26182264 3.55e-02 107_[+4(2.15e-05)]_5 chr2R:18686963-18687083 6.75e-02 120 chr2L:16921972-16922092 2.49e-02 120 chrX:13023914-13024034 2.15e-01 120 chrX:5847638-5847758 8.60e-02 6_[+2(9.58e-05)]_106 chr3R:28020732-28020852 5.85e-01 120 chr3R:17371201-17371321 1.60e-02 6_[+2(5.44e-06)]_106 chr3R:23612239-23612359 9.37e-01 120 chr3R:25854942-25855062 1.09e-01 12_[+2(1.91e-05)]_100 chr3R:24474918-24475038 9.25e-01 120 chr2L:11902634-11902754 7.41e-01 120 chr3R:13575418-13575538 1.00e+00 120 chr3L:3801483-3801603 6.90e-01 120 chr3R:27613967-27614087 8.50e-02 111_[+1(5.58e-05)]_1 chr3L:1011104-1011224 9.30e-01 120 chr3R:7334794-7334914 8.12e-02 103_[+1(1.20e-05)]_9 chr3R:31949581-31949701 1.35e-02 65_[+3(1.34e-05)]_47 chr3R:24091733-24091853 5.27e-01 120 chr2R:14726112-14726232 2.98e-02 110_[+4(6.48e-05)]_2 chr3R:14912704-14912824 3.07e-01 120 chr3L:5297357-5297477 4.13e-01 120 chr3L:10033437-10033557 2.35e-01 120 chr3R:27662132-27662252 5.07e-04 104_[+1(1.74e-05)]_8 chr3L:10482663-10482783 2.36e-01 120 chr2R:22787728-22787848 3.47e-01 120 chr3R:30550150-30550270 9.64e-01 120 chr2L:17159810-17159930 2.90e-03 76_[+1(1.74e-05)]_36 chr3R:29978741-29978861 2.27e-01 120 chr2R:18480475-18480595 9.84e-01 120 chr2R:9756279-9756399 4.29e-01 120 chr3R:15119855-15119975 6.01e-01 120 chr3R:7687007-7687127 8.53e-03 106_[+1(2.12e-05)]_6 chr2R:17918907-17919027 8.87e-01 120 chr2L:1828419-1828539 1.55e-05 95_[+1(5.58e-05)]_3_[+4(9.07e-06)]_\ 6 chr2R:12203280-12203400 8.57e-01 120 chr3R:25968638-25968758 8.49e-01 120 chrX:1706057-1706177 4.90e-01 120 chr3R:25152426-25152546 7.96e-01 120 chrX:6439607-6439727 5.13e-01 120 chrX:15304385-15304505 1.47e-03 100_[+4(4.84e-05)]_12 chrX:20797647-20797767 6.28e-02 112_[+1(7.33e-05)] chrX:6152063-6152183 5.15e-01 120 chr3R:24467393-24467513 9.91e-01 120 chr2R:23819957-23820077 1.41e-01 120 chr2R:7765171-7765291 9.99e-01 120 chr3R:29651632-29651752 2.82e-04 40_[+1(2.94e-05)]_64_[+4(8.30e-06)] chr2L:15179136-15179256 2.23e-03 4_[+2(5.44e-06)]_108 chr3R:16168250-16168370 5.19e-03 120 chr3L:3479691-3479811 5.99e-03 32_[+4(3.85e-05)]_80 chrX:10250818-10250938 2.95e-01 120 chr3R:13091831-13091951 3.83e-03 102_[+1(1.20e-05)]_10 chr3L:20848731-20848851 1.14e-01 82_[+1(7.33e-05)]_30 chr2L:13049270-13049390 4.77e-02 120 chr3R:17237082-17237202 5.69e-03 79_[+1(2.94e-05)]_33 chrX:9520354-9520474 9.99e-01 120 chr3R:14348565-14348685 9.06e-01 120 chr2L:4248425-4248545 1.28e-02 4_[+2(3.11e-05)]_108 chr2R:12739839-12739959 8.42e-02 120 chr3R:12751140-12751260 6.57e-01 120 chr2R:16916277-16916397 7.68e-01 120 chr2R:23154679-23154799 7.97e-01 120 chrX:12870036-12870156 1.00e+00 120 chr2L:2501978-2502098 3.09e-01 120 chr3L:11863722-11863842 1.00e+00 120 chr3R:8546068-8546188 7.82e-01 120 chr3R:28297636-28297756 1.06e-01 49_[+1(8.53e-05)]_63 chr3R:22822847-22822967 1.46e-02 [+2(1.91e-05)]_112 chr2R:13098830-13098950 1.87e-02 42_[+2(5.44e-06)]_70 chr3L:10599642-10599762 1.00e+00 120 chr2L:2350198-2350318 6.20e-02 120 chr3L:12874315-12874435 4.63e-02 120 chr3L:10496398-10496518 1.00e+00 120 chrX:966957-967077 8.98e-01 120 chr3R:12591843-12591963 4.17e-01 120 chrX:5143988-5144108 1.02e-02 103_[+4(6.48e-05)]_9 chr2R:16770382-16770502 1.20e-01 120 chr2L:3939000-3939120 2.78e-04 93_[+1(1.74e-05)]_19 chr3R:28118236-28118356 8.86e-01 120 chr3R:20719394-20719514 1.00e+00 120 chr3R:22503748-22503868 4.24e-04 56_[+4(3.15e-05)]_2_[+1(1.20e-05)]_\ 46 chr2L:6310055-6310175 8.29e-01 120 chr3L:11402413-11402533 7.32e-01 120 chr3R:17178289-17178409 9.11e-01 120 chr2L:18267940-18268060 8.60e-01 120 chr3L:17671909-17672029 2.43e-01 120 chr2L:2314302-2314422 2.34e-01 120 chr3R:29075788-29075908 5.80e-01 120 chr2L:17207263-17207383 2.33e-01 120 chr2R:17156231-17156351 2.45e-03 92_[+1(3.74e-06)]_20 chr2L:9864493-9864613 2.47e-01 120 chr3L:13986475-13986595 1.58e-02 33_[+3(5.45e-06)]_79 chr3R:10726867-10726987 3.75e-01 120 chr3R:8577711-8577831 9.84e-01 120 chr2L:1043736-1043856 5.59e-03 49_[+4(6.90e-05)]_63 chr3R:26671820-26671940 5.95e-01 120 chr3R:30560680-30560800 3.97e-03 30_[+4(6.48e-05)]_82 chrX:524494-524614 4.85e-02 120 chr2L:4146439-4146559 9.89e-01 120 chr2R:22976631-22976751 3.81e-02 104_[+1(3.77e-05)]_8 chr3R:18508379-18508499 7.56e-02 120 chr3R:29625990-29626110 1.00e+00 120 chr3R:18279744-18279864 3.48e-02 120 chr3R:21809065-21809185 8.84e-01 120 chr3L:2332368-2332488 4.32e-01 120 chr3L:17448082-17448202 2.61e-02 120 chr2L:7675454-7675574 6.50e-01 120 chr3L:2913421-2913541 8.48e-01 120 chr3R:8072777-8072897 2.89e-02 19_[+2(7.03e-05)]_93 chr3L:2410962-2411082 5.68e-05 1_[+4(7.73e-07)]_111 chr2R:19971489-19971609 1.46e-02 104_[+4(8.30e-06)]_8 chr2R:22789410-22789530 4.92e-01 120 chr3R:11024877-11024997 2.79e-03 83_[+1(5.58e-05)]_20_[+5(3.65e-05)]_\ 1 chr2R:10400120-10400240 1.12e-01 120 chr2L:9400327-9400447 7.89e-01 120 chr3R:26333411-26333531 9.11e-01 120 chr2R:13723377-13723497 2.52e-04 6_[+5(3.51e-06)]_106 chr2L:413132-413252 1.47e-02 120 chrX:5409005-5409125 3.30e-06 87_[+3(5.45e-06)]_5_[+5(3.51e-06)]_\ 12 chr3L:17310611-17310731 4.29e-01 120 chrX:18468005-18468125 1.80e-01 120 chr2L:2348644-2348764 2.15e-01 109_[+1(9.36e-05)]_3 chrX:9004498-9004618 9.82e-01 120 chrX:13676584-13676704 9.57e-01 120 chrX:18125719-18125839 8.01e-01 120 chrX:4691326-4691446 5.17e-01 120 chr2L:3755274-3755394 9.87e-01 120 chr3R:30325588-30325708 7.24e-01 120 chrX:3273680-3273800 1.65e-04 39_[+5(7.72e-06)]_35_[+3(3.75e-06)]_\ 30 chr2L:18186834-18186954 8.47e-01 120 chr2R:15515768-15515888 4.11e-01 120 chrX:7550883-7551003 6.12e-02 120 chr3R:15898500-15898620 7.96e-01 120 chr3R:24073883-24074003 6.87e-01 120 chrX:12073771-12073891 8.14e-01 120 chrX:4005202-4005322 2.35e-02 111_[+4(3.15e-05)]_1 chr2R:24629556-24629676 2.98e-01 120 chrX:10757768-10757888 2.50e-01 120 chr3R:31630501-31630621 5.10e-02 120 chr3R:22108476-22108596 8.43e-04 109_[+1(3.74e-06)]_3 chr2L:14141361-14141481 7.22e-01 120 chr2L:4861634-4861754 7.23e-01 120 chr3R:26494404-26494524 9.99e-01 120 chr3L:15923433-15923553 1.22e-02 29_[+2(7.03e-05)]_83 chr2L:16716972-16717092 3.13e-01 120 chrX:19818712-19818832 1.15e-03 6_[+2(1.91e-05)]_14_[+1(8.53e-05)]_\ 84 chr3R:17526219-17526339 9.96e-01 120 chr3L:19340642-19340762 5.15e-05 37_[+3(3.75e-06)]_25_[+4(1.57e-05)]_\ 42 chr3R:12543042-12543162 4.97e-01 120 chrX:17021616-17021736 8.23e-03 103_[+1(3.74e-06)]_9 chrX:2861101-2861221 4.61e-01 120 chr3L:19961919-19962039 5.91e-01 120 chr3R:28959295-28959415 2.08e-02 111_[+1(1.20e-05)]_1 chr3L:19845670-19845790 7.41e-03 63_[+3(1.34e-05)]_49 chrX:4762443-4762563 2.07e-03 72_[+1(3.74e-06)]_40 chr2L:1135642-1135762 5.14e-01 120 chr3L:1976868-1976988 3.75e-02 14_[+2(1.91e-05)]_98 chrX:19453308-19453428 9.93e-01 120 chrX:7995191-7995311 9.95e-01 120 chr2L:6868692-6868812 1.62e-01 120 chr2R:16911851-16911971 4.00e-01 120 chrX:5095705-5095825 8.83e-01 120 chr2L:20808396-20808516 3.94e-01 120 chr2R:7139390-7139510 1.72e-01 120 chr3L:8094641-8094761 8.72e-01 120 chr2L:2528210-2528330 6.31e-03 9_[+2(5.44e-06)]_103 chr3L:19969315-19969435 9.90e-01 120 chr3R:14279733-14279853 6.15e-03 24_[+2(8.39e-05)]_88 chr2L:892590-892710 1.27e-01 120 chr3L:21859830-21859950 9.99e-01 120 chr3R:31424582-31424702 3.34e-01 120 chr3L:4010217-4010337 1.12e-02 101_[+3(7.15e-06)]_11 chr2R:21895014-21895134 1.43e-02 19_[+2(5.44e-06)]_93 chr2L:20951462-20951582 3.84e-05 98_[+2(5.44e-06)]_6_[+5(7.97e-05)] chr3R:28429725-28429845 1.47e-02 112_[+1(7.33e-05)] chr2R:16778142-16778262 2.43e-01 120 chr2R:17206037-17206157 2.05e-01 120 chr2R:11144974-11145094 4.81e-02 104_[+1(3.77e-05)]_8 chr2L:11628415-11628535 9.51e-01 120 chr3R:9938621-9938741 6.92e-01 120 chr2L:4928476-4928596 2.17e-03 83_[+3(6.58e-05)]_29 chr3L:882427-882547 6.76e-02 120 chr3R:26280483-26280603 4.16e-03 17_[+2(7.14e-06)]_95 chr3R:31636669-31636789 8.66e-03 104_[+1(2.94e-05)]_8 chrX:13208113-13208233 1.15e-01 120 chr2L:1214609-1214729 8.50e-01 120 chr3L:17791657-17791777 9.42e-01 120 chr3R:16476586-16476706 5.66e-01 120 chrX:948320-948440 4.59e-04 82_[+4(1.23e-05)]_30 chr2R:15155165-15155285 4.88e-02 120 chr3L:17458969-17459089 9.97e-01 120 chrX:7488374-7488494 5.80e-01 120 chr3L:19231345-19231465 2.70e-01 120 chrX:22488377-22488497 4.27e-03 4_[+4(7.84e-05)]_108 chr3L:18837983-18838103 9.74e-03 52_[+3(3.75e-06)]_60 chr3R:10024180-10024300 2.77e-01 120 chr2L:5569650-5569770 2.74e-01 120 chr3R:23110941-23111061 5.85e-01 120 chr3R:29111897-29112017 2.85e-02 24_[+4(3.15e-05)]_88 chrX:8830281-8830401 7.29e-02 120 chr2R:24292870-24292990 4.07e-01 120 chr2L:1619317-1619437 8.60e-01 120 chr3L:2894830-2894950 4.27e-05 87_[+4(4.18e-06)]_13_[+3(5.45e-06)]_\ 4 chrX:14727706-14727826 7.58e-01 120 chr3R:30489924-30490044 1.55e-02 90_[+2(3.65e-05)]_22 chr2L:937081-937201 1.87e-02 46_[+2(1.91e-05)]_66 chrX:10184798-10184918 9.94e-01 120 chrX:20434669-20434789 4.78e-01 120 chr2L:1316562-1316682 9.38e-01 120 chr3L:3411900-3412020 1.37e-01 120 chrX:13208314-13208434 9.29e-03 90_[+5(2.51e-05)]_22 chr3L:1139529-1139649 6.81e-01 120 chr2R:15073194-15073314 9.02e-01 120 chr2R:23656700-23656820 6.42e-02 34_[+3(7.15e-06)]_78 chr2L:4292689-4292809 4.11e-05 3_[+5(7.72e-06)]_12_[+2(3.11e-05)]_\ 89 chr3L:13903372-13903492 4.59e-01 120 chr3R:30198950-30199070 1.52e-01 120 chr3L:15034374-15034494 6.78e-01 120 chr3L:19087932-19088052 3.52e-05 9_[+2(7.20e-05)]_38_[+3(3.39e-05)]_\ 57 chr2L:1837841-1837961 2.36e-02 32_[+1(3.77e-05)]_80 chrX:2161093-2161213 5.87e-06 4_[+2(5.44e-06)]_60_[+1(3.77e-05)]_\ 40 chr2L:18966965-18967085 9.91e-01 120 chr2L:19285592-19285712 1.10e-01 77_[+4(4.84e-05)]_35 chr3R:7821710-7821830 4.63e-01 120 chr2L:13461111-13461231 8.54e-01 120 chr2R:10013328-10013448 4.46e-01 120 chr2L:19930237-19930357 2.88e-02 110_[+1(2.94e-05)]_2 chr3R:19622075-19622195 3.03e-01 120 chr3L:5280083-5280203 9.04e-01 120 chr3R:18296247-18296367 4.47e-01 120 chr2R:24139214-24139334 6.59e-01 120 chr2R:7749769-7749889 2.98e-01 120 chr3R:22719626-22719746 7.30e-01 120 chrX:13817591-13817711 7.19e-01 120 chr3L:5182402-5182522 1.38e-01 109_[+1(5.58e-05)]_3 chr2L:17558267-17558387 7.20e-01 120 chrX:18004304-18004424 9.57e-01 120 chrX:2199492-2199612 5.09e-05 31_[+1(1.37e-05)]_24_[+4(4.18e-06)]_\ 49 chr3L:13912903-13913023 1.94e-02 106_[+4(4.18e-06)]_6 chrX:12937999-12938119 5.65e-01 120 chr3R:5302176-5302296 1.70e-04 9_[+4(2.40e-05)]_103 chrX:18494304-18494424 4.83e-02 112_[+1(8.53e-05)] chr3R:12657118-12657238 2.37e-02 42_[+3(1.34e-05)]_70 chr3R:26859328-26859448 1.96e-04 2_[+4(3.15e-05)]_[+2(5.44e-06)]_102 chr2L:11203751-11203871 1.45e-03 105_[+1(3.77e-05)]_7 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (5) found. ******************************************************************************** CPU: c22n04.farnam.hpc.yale.internal ********************************************************************************