******************************************************************************** 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/CG7045.fasta CONTROL SEQUENCES= --none-- ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ chr2L:4930704-4930824 1.0000 120 chr3L:19499485-19499605 1.0000 120 chr2L:1086617-1086737 1.0000 120 chr3L:17401052-17401172 1.0000 120 chr2R:17271363-17271483 1.0000 120 chr3L:12050046-12050166 1.0000 120 chr3R:18546330-18546450 1.0000 120 chr2L:13088628-13088748 1.0000 120 chr3R:30913838-30913958 1.0000 120 chr2L:8385157-8385277 1.0000 120 chr3L:5247201-5247321 1.0000 120 chr3R:26248241-26248361 1.0000 120 chr3L:3772370-3772490 1.0000 120 chr3L:11593857-11593977 1.0000 120 chr2R:21236777-21236897 1.0000 120 chr2L:8619632-8619752 1.0000 120 chr3R:7076720-7076840 1.0000 120 chr3L:4663914-4664034 1.0000 120 chr3R:17774643-17774763 1.0000 120 chr3L:11599423-11599543 1.0000 120 chr3R:15402780-15402900 1.0000 120 chr3R:21522352-21522472 1.0000 120 chr2L:18713871-18713991 1.0000 120 chr3L:3187312-3187432 1.0000 120 chr2L:1135605-1135725 1.0000 120 chr3R:20545852-20545972 1.0000 120 chrX:12778180-12778300 1.0000 120 chr3R:28025357-28025477 1.0000 120 chr2R:13293873-13293993 1.0000 120 chr2L:13156491-13156611 1.0000 120 chr3L:2426526-2426646 1.0000 120 chr2L:9754937-9755057 1.0000 120 chr2L:14398712-14398832 1.0000 120 chr3L:8985254-8985374 1.0000 120 chr3L:21846762-21846882 1.0000 120 chr3L:10504783-10504903 1.0000 120 chr2R:21649109-21649229 1.0000 120 chr3R:10330487-10330607 1.0000 120 chr3L:10110467-10110587 1.0000 120 chr3L:20884121-20884241 1.0000 120 chr3R:30084202-30084322 1.0000 120 chrX:2108745-2108865 1.0000 120 chr2L:7775394-7775514 1.0000 120 chr3R:31306580-31306700 1.0000 120 chr3L:21909021-21909141 1.0000 120 chr2R:7155825-7155945 1.0000 120 chr3R:4694972-4695092 1.0000 120 chr2L:16672406-16672526 1.0000 120 chr3L:19504829-19504949 1.0000 120 chr3R:18578095-18578215 1.0000 120 chr3R:30905682-30905802 1.0000 120 chr3L:22053469-22053589 1.0000 120 chr2L:8233784-8233904 1.0000 120 chr3R:23159725-23159845 1.0000 120 chr2L:14501770-14501890 1.0000 120 chrX:21010699-21010819 1.0000 120 chr2R:21409744-21409864 1.0000 120 chr3L:14819376-14819496 1.0000 120 chrX:11730152-11730272 1.0000 120 chr2R:12186210-12186330 1.0000 120 chr3L:5639794-5639914 1.0000 120 chr3R:13714243-13714363 1.0000 120 chr3L:12074002-12074122 1.0000 120 chr3L:17257334-17257454 1.0000 120 chr3R:7217310-7217430 1.0000 120 chr2L:5117209-5117329 1.0000 120 chr3R:17910357-17910477 1.0000 120 chr3L:9193123-9193243 1.0000 120 chr2R:10799775-10799895 1.0000 120 chr3L:9361958-9362078 1.0000 120 chr3R:12688228-12688348 1.0000 120 chr2L:9735488-9735608 1.0000 120 chr3L:16644042-16644162 1.0000 120 chr2R:20314858-20314978 1.0000 120 chr2L:7968111-7968231 1.0000 120 chr3R:26260971-26261091 1.0000 120 chrX:16569528-16569648 1.0000 120 chr3L:20353797-20353917 1.0000 120 chr3L:7835660-7835780 1.0000 120 chr2R:24747690-24747810 1.0000 120 chr2L:22108793-22108913 1.0000 120 chr3R:21195690-21195810 1.0000 120 chr3L:9421172-9421292 1.0000 120 chr2R:9184552-9184672 1.0000 120 chr2L:5303052-5303172 1.0000 120 chr3R:23667749-23667869 1.0000 120 chr2L:18985912-18986032 1.0000 120 chr2L:5890071-5890191 1.0000 120 chr2R:6993956-6994076 1.0000 120 chrX:13345471-13345591 1.0000 120 chr3R:4706190-4706310 1.0000 120 chr2R:16620776-16620896 1.0000 120 chr2R:19461664-19461784 1.0000 120 chr2L:18153235-18153355 1.0000 120 chrX:13105375-13105495 1.0000 120 chr2L:5302397-5302517 1.0000 120 chr2R:10395586-10395706 1.0000 120 chrX:16890727-16890847 1.0000 120 chr3L:7833354-7833474 1.0000 120 chr3L:5643024-5643144 1.0000 120 chr2R:15304849-15304969 1.0000 120 chr3R:21588272-21588392 1.0000 120 chrX:4691357-4691477 1.0000 120 chrX:2635197-2635317 1.0000 120 chr2R:10136174-10136294 1.0000 120 chr2L:13207222-13207342 1.0000 120 chr3L:17603681-17603801 1.0000 120 chr3R:21823178-21823298 1.0000 120 chr3L:8447933-8448053 1.0000 120 chr3L:14381706-14381826 1.0000 120 chr3L:5641719-5641839 1.0000 120 chr3L:17814164-17814284 1.0000 120 chr3R:12398221-12398341 1.0000 120 chr3R:30454354-30454474 1.0000 120 chr3R:9503787-9503907 1.0000 120 chr3R:10330808-10330928 1.0000 120 chr2L:6080513-6080633 1.0000 120 chr3R:9946576-9946696 1.0000 120 chr3R:18438330-18438450 1.0000 120 chr3L:8979170-8979290 1.0000 120 chr2L:3059329-3059449 1.0000 120 chr3R:26987643-26987763 1.0000 120 chr2R:9830278-9830398 1.0000 120 chr3R:25268432-25268552 1.0000 120 chr2L:19415952-19416072 1.0000 120 chr2R:10045462-10045582 1.0000 120 chr3L:9503959-9504079 1.0000 120 chr3L:19496085-19496205 1.0000 120 chr2L:5618137-5618257 1.0000 120 chr3R:10111702-10111822 1.0000 120 chr2R:8120588-8120708 1.0000 120 chrX:21519358-21519478 1.0000 120 chr2R:19373817-19373937 1.0000 120 chr2L:13461018-13461138 1.0000 120 chr3R:5839099-5839219 1.0000 120 chr3L:9398554-9398674 1.0000 120 chr3L:8453919-8454039 1.0000 120 chr3R:10679262-10679382 1.0000 120 chr3R:25280113-25280233 1.0000 120 chr3R:15366994-15367114 1.0000 120 chr2L:20431342-20431462 1.0000 120 chr3L:16804758-16804878 1.0000 120 chr2R:15846374-15846494 1.0000 120 chr3L:2800418-2800538 1.0000 120 chr2L:9737875-9737995 1.0000 120 chr2L:13801299-13801419 1.0000 120 chr3R:22518420-22518540 1.0000 120 chr3L:15996940-15997060 1.0000 120 chr2L:1048578-1048698 1.0000 120 chr3R:14217960-14218080 1.0000 120 chr2L:3507601-3507721 1.0000 120 chr2L:14336601-14336721 1.0000 120 chr2L:18548925-18549045 1.0000 120 chr2R:11423538-11423658 1.0000 120 chr2L:9526628-9526748 1.0000 120 chr3L:3940706-3940826 1.0000 120 chr2R:10553802-10553922 1.0000 120 chr2R:23672654-23672774 1.0000 120 chr2L:10849704-10849824 1.0000 120 chr2L:1731039-1731159 1.0000 120 chr2R:7731061-7731181 1.0000 120 chr3R:8577744-8577864 1.0000 120 chrX:2685335-2685455 1.0000 120 chr3R:21193910-21194030 1.0000 120 chr3R:22455854-22455974 1.0000 120 chr3R:11173261-11173381 1.0000 120 chr3R:8654244-8654364 1.0000 120 chr3L:17956596-17956716 1.0000 120 chr3L:17001182-17001302 1.0000 120 chr3R:8712821-8712941 1.0000 120 chr3R:27662154-27662274 1.0000 120 chr2L:18459804-18459924 1.0000 120 chr2L:13206357-13206477 1.0000 120 chr3R:13819187-13819307 1.0000 120 chr2L:9669487-9669607 1.0000 120 chr3L:9065034-9065154 1.0000 120 chr3R:10380106-10380226 1.0000 120 chr3R:10311699-10311819 1.0000 120 chr3R:18169142-18169262 1.0000 120 chr3R:11178504-11178624 1.0000 120 chr3R:5694577-5694697 1.0000 120 chr2L:16530184-16530304 1.0000 120 chr3R:26801502-26801622 1.0000 120 chr2L:2956458-2956578 1.0000 120 chr3R:25855739-25855859 1.0000 120 chr3R:21157229-21157349 1.0000 120 chr3R:20549075-20549195 1.0000 120 chrX:3675690-3675810 1.0000 120 chr3R:23067479-23067599 1.0000 120 chr2L:18441117-18441237 1.0000 120 chr3R:31250583-31250703 1.0000 120 chr3L:21321946-21322066 1.0000 120 chrX:15313997-15314117 1.0000 120 chr3L:3209067-3209187 1.0000 120 chr3R:19924414-19924534 1.0000 120 chr2R:12279568-12279688 1.0000 120 chr3R:26009846-26009966 1.0000 120 chr2L:1970817-1970937 1.0000 120 chr2L:4417072-4417192 1.0000 120 chr2L:5007427-5007547 1.0000 120 chr2R:22373587-22373707 1.0000 120 chrX:16086217-16086337 1.0000 120 chr2L:9010426-9010546 1.0000 120 chr3R:26259072-26259192 1.0000 120 chr3R:9075035-9075155 1.0000 120 chr3L:10756199-10756319 1.0000 120 chr3L:12075074-12075194 1.0000 120 chr2R:17870044-17870164 1.0000 120 chr2L:18632448-18632568 1.0000 120 chr3R:23164278-23164398 1.0000 120 chrX:3265979-3266099 1.0000 120 chr2L:8163882-8164002 1.0000 120 chr2L:9459415-9459535 1.0000 120 chrX:2107941-2108061 1.0000 120 chr3L:2572130-2572250 1.0000 120 chr3R:14680518-14680638 1.0000 120 chr3L:11656315-11656435 1.0000 120 chr3L:9466603-9466723 1.0000 120 chr2L:435575-435695 1.0000 120 chr3L:19044935-19045055 1.0000 120 chr3R:14285734-14285854 1.0000 120 chr3L:21343385-21343505 1.0000 120 chr3L:17049907-17050027 1.0000 120 chrX:9466265-9466385 1.0000 120 chr3L:751939-752059 1.0000 120 chr2L:5003159-5003279 1.0000 120 chr2L:125509-125629 1.0000 120 chr3R:24626344-24626464 1.0000 120 chr3R:21931489-21931609 1.0000 120 chr3L:17000468-17000588 1.0000 120 chr3R:9430498-9430618 1.0000 120 chr3L:5359428-5359548 1.0000 120 chr3R:15898469-15898589 1.0000 120 chr3L:5807517-5807637 1.0000 120 chrX:11146949-11147069 1.0000 120 chr3L:21636729-21636849 1.0000 120 chr2R:24963337-24963457 1.0000 120 chr3R:12442608-12442728 1.0000 120 chr2R:22789381-22789501 1.0000 120 chr2R:24749560-24749680 1.0000 120 chr3R:30308228-30308348 1.0000 120 chr3L:21892343-21892463 1.0000 120 chr2L:12002155-12002275 1.0000 120 chr2R:17405092-17405212 1.0000 120 chr2L:7968312-7968432 1.0000 120 chr2L:11736164-11736284 1.0000 120 chr2L:13839055-13839175 1.0000 120 chr2L:17448566-17448686 1.0000 120 chr2R:14073604-14073724 1.0000 120 chr2R:10272889-10273009 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_CG7045/ -dna -nmotifs 5 -w 8 -maxsize 250000 -nostatus ../result/final_prediction/fly/fasta/RankLinear8.0_60/CG7045.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 0.316 C 0.181 G 0.184 T 0.32 Background letter frequencies (from file dataset with add-one prior applied): A 0.316 C 0.181 G 0.184 T 0.32 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF CCRCCCCC MEME-1 width = 8 sites = 13 llr = 141 E-value = 4.0e-002 ******************************************************************************** -------------------------------------------------------------------------------- Motif CCRCCCCC MEME-1 Description -------------------------------------------------------------------------------- Simplified A ::5:1::: pos.-specific C 8a2a89aa probability G 2:3::1:: matrix T ::::2::: bits 2.5 * * ** 2.2 * * ** 2.0 * * *** 1.7 ** * *** Relative 1.5 ** * *** Entropy 1.2 ** ***** (15.7 bits) 1.0 ** ***** 0.7 ** ***** 0.5 ******** 0.2 ******** 0.0 -------- Multilevel CCACCCCC consensus G sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCRCCCCC MEME-1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr2L:17448566-17448686 28 3.18e-06 TCCACGAGCC CCACCCCC TCTGGGCCCC chr3R:30308228-30308348 14 3.18e-06 CCCACCTCCC CCACCCCC CCACGCAAGC chr3L:5641719-5641839 86 3.18e-06 AGGGTTGCCG CCACCCCC CCTGAAAAAC chr2L:22108793-22108913 58 3.18e-06 GTTCTCTTTG CCGCCCCC CTTGAGCACT chr3L:5639794-5639914 101 3.18e-06 CATCCCCCCT CCACCCCC ACCAACCCCT chr3L:17401052-17401172 100 3.18e-06 TGCACCAGCA CCACCCCC CTTTTGGGGG chr3L:12075074-12075194 32 4.33e-06 GAATAGCTAA CCCCCCCC TCCCCCTCTT chr3R:12688228-12688348 90 7.57e-06 ATCGCTATTT GCGCCCCC GACAAATGAA chr2L:1970817-1970937 57 1.32e-05 CCTCGACACC CCGCTCCC ATCACTCGTG chr2L:6080513-6080633 43 1.32e-05 TGATTGCGAA CCACTCCC GCCAGCCCCC chr3R:26260971-26261091 46 1.44e-05 AGTTCGCGTA GCCCCCCC ACTCCTTCAA chr3R:22518420-22518540 77 1.76e-05 CCACCCCTCG CCGCCGCC CACAGTGGGC chr3L:3940706-3940826 112 2.52e-05 AAAATATTTG CCACACCC T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCRCCCCC MEME-1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr2L:17448566-17448686 3.2e-06 27_[+1]_85 chr3R:30308228-30308348 3.2e-06 13_[+1]_99 chr3L:5641719-5641839 3.2e-06 85_[+1]_27 chr2L:22108793-22108913 3.2e-06 57_[+1]_55 chr3L:5639794-5639914 3.2e-06 100_[+1]_12 chr3L:17401052-17401172 3.2e-06 99_[+1]_13 chr3L:12075074-12075194 4.3e-06 31_[+1]_81 chr3R:12688228-12688348 7.6e-06 89_[+1]_23 chr2L:1970817-1970937 1.3e-05 56_[+1]_56 chr2L:6080513-6080633 1.3e-05 42_[+1]_70 chr3R:26260971-26261091 1.4e-05 45_[+1]_67 chr3R:22518420-22518540 1.8e-05 76_[+1]_36 chr3L:3940706-3940826 2.5e-05 111_[+1]_1 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCRCCCCC MEME-1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF CCRCCCCC width=8 seqs=13 chr2L:17448566-17448686 ( 28) CCACCCCC 1 chr3R:30308228-30308348 ( 14) CCACCCCC 1 chr3L:5641719-5641839 ( 86) CCACCCCC 1 chr2L:22108793-22108913 ( 58) CCGCCCCC 1 chr3L:5639794-5639914 ( 101) CCACCCCC 1 chr3L:17401052-17401172 ( 100) CCACCCCC 1 chr3L:12075074-12075194 ( 32) CCCCCCCC 1 chr3R:12688228-12688348 ( 90) GCGCCCCC 1 chr2L:1970817-1970937 ( 57) CCGCTCCC 1 chr2L:6080513-6080633 ( 43) CCACTCCC 1 chr3R:26260971-26261091 ( 46) GCCCCCCC 1 chr3R:22518420-22518540 ( 77) CCGCCGCC 1 chr3L:3940706-3940826 ( 112) CCACACCC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCRCCCCC MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 28250 bayes= 12.7154 E= 4.0e-002 -1035 223 -26 -1035 -1035 247 -1035 -1035 77 -23 74 -1035 -1035 247 -1035 -1035 -203 209 -1035 -105 -1035 235 -126 -1035 -1035 247 -1035 -1035 -1035 247 -1035 -1035 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCRCCCCC MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 13 E= 4.0e-002 0.000000 0.846154 0.153846 0.000000 0.000000 1.000000 0.000000 0.000000 0.538462 0.153846 0.307692 0.000000 0.000000 1.000000 0.000000 0.000000 0.076923 0.769231 0.000000 0.153846 0.000000 0.923077 0.076923 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCRCCCCC MEME-1 regular expression -------------------------------------------------------------------------------- CC[AG]CCCCC -------------------------------------------------------------------------------- Time 7.42 secs. ******************************************************************************** ******************************************************************************** MOTIF SCCRCTGY MEME-2 width = 8 sites = 15 llr = 149 E-value = 2.3e+003 ******************************************************************************** -------------------------------------------------------------------------------- Motif SCCRCTGY MEME-2 Description -------------------------------------------------------------------------------- Simplified A :::7:::: pos.-specific C 5aa:9::5 probability G 5::31:a1 matrix T :::::a:4 bits 2.5 ** * 2.2 ** * * 2.0 ** * * 1.7 ** *** Relative 1.5 *** *** Entropy 1.2 *** *** (14.3 bits) 1.0 ******* 0.7 ******** 0.5 ******** 0.2 ******** 0.0 -------- Multilevel CCCACTGC consensus G G T sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif SCCRCTGY MEME-2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr2R:14073604-14073724 102 3.61e-06 AAAGTAAATA CCCACTGC CGATGGACTG chr3R:21823178-21823298 43 3.61e-06 TTGATAAATA CCCACTGC ATGCTTAATA chr2L:17448566-17448686 107 9.39e-06 ACGTCGAAAA GCCACTGC GACTGC chr2R:12279568-12279688 84 9.39e-06 CGTTGTAgct gccactgc tactgctgct chr3R:26259072-26259192 77 1.15e-05 CACTTTTATT GCCGCTGC TGCTGCGCTG chr2R:13293873-13293993 66 1.15e-05 TTACTCATTA GCCGCTGC ATTTGGCTCA chr3R:14285734-14285854 113 1.79e-05 TCAACGAGGT CCCACTGT chr3R:14680518-14680638 1 1.79e-05 . CCCACTGT TGGCCTCGTC chr3R:22455854-22455974 91 1.79e-05 ACTTTGATGG CCCACTGT GAACTATGAA chr3L:5639794-5639914 75 1.79e-05 CTTACACACA CCCACTGT GCGGCCTGCA chr3R:30454354-30454474 66 2.16e-05 TCGTGTGACC CCCGCTGT TCATTCATTC chrX:9466265-9466385 77 3.19e-05 ACGCAGTGTT GCCGCTGT TGAAAATTTT chr3L:22053469-22053589 91 4.15e-05 TTAAGGCAAC GCCACTGG GCCACCAAAT chr2L:12002155-12002275 35 4.36e-05 CTTGCCGATC GCCGCTGG TTAACTAATC chr3L:751939-752059 58 4.73e-05 AAACATTTTT CCCAGTGC CAAAGAACTC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif SCCRCTGY MEME-2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr2R:14073604-14073724 3.6e-06 101_[+2]_11 chr3R:21823178-21823298 3.6e-06 42_[+2]_70 chr2L:17448566-17448686 9.4e-06 106_[+2]_6 chr2R:12279568-12279688 9.4e-06 83_[+2]_29 chr3R:26259072-26259192 1.2e-05 76_[+2]_36 chr2R:13293873-13293993 1.2e-05 65_[+2]_47 chr3R:14285734-14285854 1.8e-05 112_[+2] chr3R:14680518-14680638 1.8e-05 [+2]_112 chr3R:22455854-22455974 1.8e-05 90_[+2]_22 chr3L:5639794-5639914 1.8e-05 74_[+2]_38 chr3R:30454354-30454474 2.2e-05 65_[+2]_47 chrX:9466265-9466385 3.2e-05 76_[+2]_36 chr3L:22053469-22053589 4.1e-05 90_[+2]_22 chr2L:12002155-12002275 4.4e-05 34_[+2]_78 chr3L:751939-752059 4.7e-05 57_[+2]_55 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif SCCRCTGY MEME-2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF SCCRCTGY width=8 seqs=15 chr2R:14073604-14073724 ( 102) CCCACTGC 1 chr3R:21823178-21823298 ( 43) CCCACTGC 1 chr2L:17448566-17448686 ( 107) GCCACTGC 1 chr2R:12279568-12279688 ( 84) GCCACTGC 1 chr3R:26259072-26259192 ( 77) GCCGCTGC 1 chr2R:13293873-13293993 ( 66) GCCGCTGC 1 chr3R:14285734-14285854 ( 113) CCCACTGT 1 chr3R:14680518-14680638 ( 1) CCCACTGT 1 chr3R:22455854-22455974 ( 91) CCCACTGT 1 chr3L:5639794-5639914 ( 75) CCCACTGT 1 chr3R:30454354-30454474 ( 66) CCCGCTGT 1 chrX:9466265-9466385 ( 77) GCCGCTGT 1 chr3L:22053469-22053589 ( 91) GCCACTGG 1 chr2L:12002155-12002275 ( 35) GCCGCTGG 1 chr3L:751939-752059 ( 58) CCCAGTGC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif SCCRCTGY MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 28250 bayes= 12.5841 E= 2.3e+003 -1055 156 134 -1055 -1055 247 -1055 -1055 -1055 247 -1055 -1055 108 -1055 86 -1055 -1055 237 -146 -1055 -1055 -1055 -1055 165 -1055 -1055 244 -1055 -1055 137 -46 32 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif SCCRCTGY MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 15 E= 2.3e+003 0.000000 0.533333 0.466667 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.666667 0.000000 0.333333 0.000000 0.000000 0.933333 0.066667 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.466667 0.133333 0.400000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif SCCRCTGY MEME-2 regular expression -------------------------------------------------------------------------------- [CG]CC[AG]CTG[CT] -------------------------------------------------------------------------------- Time 13.70 secs. ******************************************************************************** ******************************************************************************** MOTIF DSNGCWGC MEME-3 width = 8 sites = 47 llr = 373 E-value = 1.6e+003 ******************************************************************************** -------------------------------------------------------------------------------- Motif DSNGCWGC MEME-3 Description -------------------------------------------------------------------------------- Simplified A 3:3::4:: pos.-specific C :622a::a probability G 4438:2a: matrix T 3:2::3:: bits 2.5 * ** 2.2 * ** 2.0 * ** 1.7 ** ** Relative 1.5 * ** ** Entropy 1.2 * ** ** (11.4 bits) 1.0 * ** ** 0.7 * ** ** 0.5 ** ** ** 0.2 ** ***** 0.0 -------- Multilevel GCGGCAGC consensus TGA T sequence A G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif DSNGCWGC MEME-3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr3L:5807517-5807637 48 3.40e-06 CATTGAAGAG GCGGCGGC CAGGGGCCGA chr3L:17049907-17050027 8 9.87e-06 CGGCAAA GCCGCAGC CAATGGTCAT chr3R:9946576-9946696 70 1.48e-05 GGTTGATTCA GGGGCGGC GTCGAGGGGT chr2L:13207222-13207342 72 1.48e-05 AAAAGCTGAC GCAGCAGC GTTCATAATT chr2L:8619632-8619752 83 1.48e-05 agcagcatca gcagcagc accagcTTGT chr3L:17956596-17956716 104 1.83e-05 TTAGTTTCTA GGGGCTGC TCTCTCGCT chr2R:11423538-11423658 20 1.83e-05 TTTATATCTT GGGGCTGC TTTCAGGAAG chr3R:20549075-20549195 30 3.59e-05 ATCTATTGAA GGCGCAGC AGAGTGCTCC chr3R:13819187-13819307 50 3.59e-05 CTGGTGGGGT GGCGCAGC ACCTGTGCAA chr2R:10553802-10553922 74 3.59e-05 GTTAGTAGTT GCAGCTGC AAGGTGCTAT chrX:11146949-11147069 11 4.89e-05 CGGAAAACCC ACGGCGGC TCTGACCCAC chr3L:21343385-21343505 8 4.89e-05 TACGTGA TCGGCGGC TCCCCATTCC chr2L:8385157-8385277 84 6.08e-05 TTGACATAAG TCGGCTGC TTGTCTGGAT chr2L:1135605-1135725 87 7.43e-05 CATATATCAA GCTGCGGC TTAAAGCACA chr2L:18713871-18713991 101 7.43e-05 ATACGTCGGG AGGGCAGC ACAATCTTTT chr2L:7968312-7968432 95 8.75e-05 TATTATTTTT GCTGCTGC CCAATGTTCA chr2L:9459415-9459535 83 8.75e-05 AGCCCGTGTC ACCGCAGC GCTGGGAAAA chr2R:12279568-12279688 96 8.75e-05 cactgctact gctgctgc tgTGTCGTCG chrX:16569528-16569648 88 8.75e-05 GCTAACAATC ACCGCAGC GGTTGCACAA chr3R:14680518-14680638 44 1.08e-04 TGCGGAGAAA TGGGCGGC AATTAAAGCT chr2L:18441117-18441237 32 1.08e-04 GGGCTATTTA GGTGCAGC CTGGAAAAAA chr2L:9737875-9737995 12 1.08e-04 CACTGCGATA ACAGCAGC TATTTGTTGT chr3R:5839099-5839219 109 1.08e-04 TTGGCGACAA TCAGCAGC AAGA chr2R:10799775-10799895 12 1.08e-04 CTCAGTGCCC ACAGCAGC TACAGTGGAG chrX:21010699-21010819 70 1.08e-04 AAATAAAACA ACAGCAGC TTACGACTTT chr3R:23164278-23164398 86 1.22e-04 CAGGAGTCAT GCGCCGGC CAagatccag chr2L:18459804-18459924 11 1.22e-04 GAGCAAACAA AGGGCTGC GGAAAATGTT chr3L:19496085-19496205 40 1.41e-04 AAATTTGCCA GCGCCTGC ACTTTCGCTT chr2L:9526628-9526748 100 1.67e-04 TTTTGTTTTA TCAGCTGC AGAAAGTATA chr2L:14336601-14336721 45 1.67e-04 GTTTGTCGCT TCAGCTGC GTAAACATTT chr3R:27662154-27662274 59 1.82e-04 CCTTACACGG AGAGCAGC CTTTTTTCCC chr2L:3059329-3059449 21 2.04e-04 AAGCTCCGAC TGCGCGGC ATCACCTGAT chr2R:20314858-20314978 103 2.04e-04 TTAGTGTATT GCACCAGC CCAAGGTTAT chr3L:17401052-17401172 91 2.04e-04 CTTTGCAATT GCACCAGC ACCACCCCCC chr3L:19499485-19499605 25 2.23e-04 AAATCTTTAT AGCGCTGC CGCAGTTGCT chrX:2107941-2108061 98 2.48e-04 AAATGAAAAG ACTGCGGC CGTTCATAGA chr3R:8712821-8712941 101 2.48e-04 CTTTAGCGGC GCCCCTGC TGATAAGTCA chr2R:15846374-15846494 102 2.48e-04 TTTACCTAGC TGAGCTGC TTTATAACTT chr3L:12050046-12050166 14 2.48e-04 AAGTTGAAGT AGAGCTGC TTGGAAATAC chr3R:14285734-14285854 86 2.74e-04 AATGCTACCA TCTGCTGC TAGTCGCACT chr3L:19044935-19045055 46 2.74e-04 GATTTGTTTT TCGCCAGC CGTTTTGTTG chr3R:9430498-9430618 108 2.91e-04 TTCTTGTTCC TGTGCAGC GCATG chr2L:4417072-4417192 109 2.91e-04 TTTTTCGCAC AGTGCAGC AGAC chr3L:5641719-5641839 18 2.91e-04 TGTTGATATT TGTGCAGC AAGGCATACA chr2L:13088628-13088748 113 3.00e-04 CGCATCGCTT GGCCCGGC chr3R:26260971-26261091 28 3.19e-04 AGGCTTCTTA TCGCCTGC AGTTCGCGTA chr3L:17814164-17814284 21 3.46e-04 TATCGTTAAG TGGCCAGC AGATTAAATT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif DSNGCWGC MEME-3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr3L:5807517-5807637 3.4e-06 47_[+3]_65 chr3L:17049907-17050027 9.9e-06 7_[+3]_105 chr3R:9946576-9946696 1.5e-05 69_[+3]_43 chr2L:13207222-13207342 1.5e-05 71_[+3]_41 chr2L:8619632-8619752 1.5e-05 82_[+3]_30 chr3L:17956596-17956716 1.8e-05 103_[+3]_9 chr2R:11423538-11423658 1.8e-05 19_[+3]_93 chr3R:20549075-20549195 3.6e-05 29_[+3]_83 chr3R:13819187-13819307 3.6e-05 49_[+3]_63 chr2R:10553802-10553922 3.6e-05 73_[+3]_39 chrX:11146949-11147069 4.9e-05 10_[+3]_102 chr3L:21343385-21343505 4.9e-05 7_[+3]_105 chr2L:8385157-8385277 6.1e-05 83_[+3]_29 chr2L:1135605-1135725 7.4e-05 86_[+3]_26 chr2L:18713871-18713991 7.4e-05 100_[+3]_12 chr2L:7968312-7968432 8.8e-05 94_[+3]_18 chr2L:9459415-9459535 8.8e-05 82_[+3]_30 chr2R:12279568-12279688 8.8e-05 95_[+3]_17 chrX:16569528-16569648 8.8e-05 87_[+3]_25 chr3R:14680518-14680638 0.00011 43_[+3]_69 chr2L:18441117-18441237 0.00011 31_[+3]_81 chr2L:9737875-9737995 0.00011 11_[+3]_101 chr3R:5839099-5839219 0.00011 108_[+3]_4 chr2R:10799775-10799895 0.00011 11_[+3]_101 chrX:21010699-21010819 0.00011 69_[+3]_43 chr3R:23164278-23164398 0.00012 85_[+3]_27 chr2L:18459804-18459924 0.00012 10_[+3]_102 chr3L:19496085-19496205 0.00014 39_[+3]_73 chr2L:9526628-9526748 0.00017 99_[+3]_13 chr2L:14336601-14336721 0.00017 44_[+3]_68 chr3R:27662154-27662274 0.00018 58_[+3]_54 chr2L:3059329-3059449 0.0002 20_[+3]_92 chr2R:20314858-20314978 0.0002 102_[+3]_10 chr3L:17401052-17401172 0.0002 90_[+3]_22 chr3L:19499485-19499605 0.00022 24_[+3]_88 chrX:2107941-2108061 0.00025 97_[+3]_15 chr3R:8712821-8712941 0.00025 100_[+3]_12 chr2R:15846374-15846494 0.00025 101_[+3]_11 chr3L:12050046-12050166 0.00025 13_[+3]_99 chr3R:14285734-14285854 0.00027 85_[+3]_27 chr3L:19044935-19045055 0.00027 45_[+3]_67 chr3R:9430498-9430618 0.00029 107_[+3]_5 chr2L:4417072-4417192 0.00029 108_[+3]_4 chr3L:5641719-5641839 0.00029 17_[+3]_95 chr2L:13088628-13088748 0.0003 112_[+3] chr3R:26260971-26261091 0.00032 27_[+3]_85 chr3L:17814164-17814284 0.00035 20_[+3]_92 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif DSNGCWGC MEME-3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF DSNGCWGC width=8 seqs=47 chr3L:5807517-5807637 ( 48) GCGGCGGC 1 chr3L:17049907-17050027 ( 8) GCCGCAGC 1 chr3R:9946576-9946696 ( 70) GGGGCGGC 1 chr2L:13207222-13207342 ( 72) GCAGCAGC 1 chr2L:8619632-8619752 ( 83) GCAGCAGC 1 chr3L:17956596-17956716 ( 104) GGGGCTGC 1 chr2R:11423538-11423658 ( 20) GGGGCTGC 1 chr3R:20549075-20549195 ( 30) GGCGCAGC 1 chr3R:13819187-13819307 ( 50) GGCGCAGC 1 chr2R:10553802-10553922 ( 74) GCAGCTGC 1 chrX:11146949-11147069 ( 11) ACGGCGGC 1 chr3L:21343385-21343505 ( 8) TCGGCGGC 1 chr2L:8385157-8385277 ( 84) TCGGCTGC 1 chr2L:1135605-1135725 ( 87) GCTGCGGC 1 chr2L:18713871-18713991 ( 101) AGGGCAGC 1 chr2L:7968312-7968432 ( 95) GCTGCTGC 1 chr2L:9459415-9459535 ( 83) ACCGCAGC 1 chr2R:12279568-12279688 ( 96) GCTGCTGC 1 chrX:16569528-16569648 ( 88) ACCGCAGC 1 chr3R:14680518-14680638 ( 44) TGGGCGGC 1 chr2L:18441117-18441237 ( 32) GGTGCAGC 1 chr2L:9737875-9737995 ( 12) ACAGCAGC 1 chr3R:5839099-5839219 ( 109) TCAGCAGC 1 chr2R:10799775-10799895 ( 12) ACAGCAGC 1 chrX:21010699-21010819 ( 70) ACAGCAGC 1 chr3R:23164278-23164398 ( 86) GCGCCGGC 1 chr2L:18459804-18459924 ( 11) AGGGCTGC 1 chr3L:19496085-19496205 ( 40) GCGCCTGC 1 chr2L:9526628-9526748 ( 100) TCAGCTGC 1 chr2L:14336601-14336721 ( 45) TCAGCTGC 1 chr3R:27662154-27662274 ( 59) AGAGCAGC 1 chr2L:3059329-3059449 ( 21) TGCGCGGC 1 chr2R:20314858-20314978 ( 103) GCACCAGC 1 chr3L:17401052-17401172 ( 91) GCACCAGC 1 chr3L:19499485-19499605 ( 25) AGCGCTGC 1 chrX:2107941-2108061 ( 98) ACTGCGGC 1 chr3R:8712821-8712941 ( 101) GCCCCTGC 1 chr2R:15846374-15846494 ( 102) TGAGCTGC 1 chr3L:12050046-12050166 ( 14) AGAGCTGC 1 chr3R:14285734-14285854 ( 86) TCTGCTGC 1 chr3L:19044935-19045055 ( 46) TCGCCAGC 1 chr3R:9430498-9430618 ( 108) TGTGCAGC 1 chr2L:4417072-4417192 ( 109) AGTGCAGC 1 chr3L:5641719-5641839 ( 18) TGTGCAGC 1 chr2L:13088628-13088748 ( 113) GGCCCGGC 1 chr3R:26260971-26261091 ( 28) TCGCCTGC 1 chr3L:17814164-17814284 ( 21) TGGCCAGC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif DSNGCWGC MEME-3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 28250 bayes= 11.13 E= 1.6e+003 -19 -1220 121 -10 -1220 172 114 -1220 -8 8 80 -74 -1220 8 214 -1220 -1220 247 -1220 -1220 50 -1220 21 9 -1220 -1220 244 -1220 -1220 247 -1220 -1220 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif DSNGCWGC MEME-3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 47 E= 1.6e+003 0.276596 0.000000 0.425532 0.297872 0.000000 0.595745 0.404255 0.000000 0.297872 0.191489 0.319149 0.191489 0.000000 0.191489 0.808511 0.000000 0.000000 1.000000 0.000000 0.000000 0.446809 0.000000 0.212766 0.340426 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif DSNGCWGC MEME-3 regular expression -------------------------------------------------------------------------------- [GTA][CG][GA]GC[ATG]GC -------------------------------------------------------------------------------- Time 20.44 secs. ******************************************************************************** ******************************************************************************** MOTIF GGCAAAYA MEME-4 width = 8 sites = 17 llr = 163 E-value = 1.8e+004 ******************************************************************************** -------------------------------------------------------------------------------- Motif GGCAAAYA MEME-4 Description -------------------------------------------------------------------------------- Simplified A 1::aaa:a pos.-specific C ::a:::5: probability G 8a:::::: matrix T 1:::::5: bits 2.5 ** 2.2 ** 2.0 ** 1.7 ***** * Relative 1.5 ***** * Entropy 1.2 ****** * (13.8 bits) 1.0 ******** 0.7 ******** 0.5 ******** 0.2 ******** 0.0 -------- Multilevel GGCAAATA consensus C sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGCAAAYA MEME-4 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr3R:8654244-8654364 70 1.11e-05 AAATTTATCT GGCAAACA AACAACGACA chr3R:25280113-25280233 31 1.11e-05 GGCTTTTATG GGCAAACA AGCCTGCGAT chr3L:8447933-8448053 43 1.11e-05 GAAAACGCTG GGCAAACA ATAAAAAGCT chr3R:10330487-10330607 40 1.11e-05 GGGCCTAGCA GGCAAACA ATTGGAATTT chr2R:10272889-10273009 31 3.06e-05 GTTTTGGCTT GGCAAATA AAACACACAA chr3R:19924414-19924534 71 3.06e-05 ATTTGTCGAG GGCAAATA TGGCGAAAGA chr3R:13819187-13819307 80 3.06e-05 CTGGCCACTT GGCAAATA AATTGCGTAA chr3R:21588272-21588392 62 3.06e-05 GTTTGTCCAC GGCAAATA TTTGCGGCAA chr2R:6993956-6994076 55 3.06e-05 TTATACGATT GGCAAATA TCATATACGA chr2R:21649109-21649229 5 3.06e-05 AGTT GGCAAATA TGCACTCTGC chr3R:20545852-20545972 28 3.06e-05 GTTGGTTGCA GGCAAATA TGTTAGTCGG chr2L:18713871-18713991 72 3.06e-05 TCCTAAGTCT GGCAAATA TTTCACTTTT chr3R:17774643-17774763 13 3.06e-05 GATTATTGTT GGCAAATA TAAACAAATA chr3R:9946576-9946696 18 4.96e-05 CCAAAGCCAA AGCAAACA GGCAAATTAT chr3L:10110467-10110587 68 4.96e-05 ATTCAATTAT AGCAAACA ATTTGATTGA chr2R:23672654-23672774 67 6.88e-05 GCGGAGCTTA TGCAAACA ACTTGTTATT chr3R:18438330-18438450 73 6.88e-05 TTGCTATGAA TGCAAACA CAAAGTTGTT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGCAAAYA MEME-4 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr3R:8654244-8654364 1.1e-05 69_[+4]_43 chr3R:25280113-25280233 1.1e-05 30_[+4]_82 chr3L:8447933-8448053 1.1e-05 42_[+4]_70 chr3R:10330487-10330607 1.1e-05 39_[+4]_73 chr2R:10272889-10273009 3.1e-05 30_[+4]_82 chr3R:19924414-19924534 3.1e-05 70_[+4]_42 chr3R:13819187-13819307 3.1e-05 79_[+4]_33 chr3R:21588272-21588392 3.1e-05 61_[+4]_51 chr2R:6993956-6994076 3.1e-05 54_[+4]_58 chr2R:21649109-21649229 3.1e-05 4_[+4]_108 chr3R:20545852-20545972 3.1e-05 27_[+4]_85 chr2L:18713871-18713991 3.1e-05 71_[+4]_41 chr3R:17774643-17774763 3.1e-05 12_[+4]_100 chr3R:9946576-9946696 5e-05 17_[+4]_95 chr3L:10110467-10110587 5e-05 67_[+4]_45 chr2R:23672654-23672774 6.9e-05 66_[+4]_46 chr3R:18438330-18438450 6.9e-05 72_[+4]_40 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGCAAAYA MEME-4 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF GGCAAAYA width=8 seqs=17 chr3R:8654244-8654364 ( 70) GGCAAACA 1 chr3R:25280113-25280233 ( 31) GGCAAACA 1 chr3L:8447933-8448053 ( 43) GGCAAACA 1 chr3R:10330487-10330607 ( 40) GGCAAACA 1 chr2R:10272889-10273009 ( 31) GGCAAATA 1 chr3R:19924414-19924534 ( 71) GGCAAATA 1 chr3R:13819187-13819307 ( 80) GGCAAATA 1 chr3R:21588272-21588392 ( 62) GGCAAATA 1 chr2R:6993956-6994076 ( 55) GGCAAATA 1 chr2R:21649109-21649229 ( 5) GGCAAATA 1 chr3R:20545852-20545972 ( 28) GGCAAATA 1 chr2L:18713871-18713991 ( 72) GGCAAATA 1 chr3R:17774643-17774763 ( 13) GGCAAATA 1 chr3R:9946576-9946696 ( 18) AGCAAACA 1 chr3L:10110467-10110587 ( 68) AGCAAACA 1 chr2R:23672654-23672774 ( 67) TGCAAACA 1 chr3R:18438330-18438450 ( 73) TGCAAACA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGCAAAYA MEME-4 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 28250 bayes= 9.9265 E= 1.8e+004 -142 -1073 206 -144 -1073 -1073 244 -1073 -1073 247 -1073 -1073 166 -1073 -1073 -1073 166 -1073 -1073 -1073 166 -1073 -1073 -1073 -1073 138 -1073 73 166 -1073 -1073 -1073 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGCAAAYA MEME-4 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 17 E= 1.8e+004 0.117647 0.000000 0.764706 0.117647 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.470588 0.000000 0.529412 1.000000 0.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGCAAAYA MEME-4 regular expression -------------------------------------------------------------------------------- GGCAAA[TC]A -------------------------------------------------------------------------------- Time 26.59 secs. ******************************************************************************** ******************************************************************************** MOTIF KGGTGGSG MEME-5 width = 8 sites = 19 llr = 179 E-value = 1.5e+004 ******************************************************************************** -------------------------------------------------------------------------------- Motif KGGTGGSG MEME-5 Description -------------------------------------------------------------------------------- Simplified A 2::::::: pos.-specific C :12:::3: probability G 4983aa5a matrix T 4::7::2: bits 2.5 ** * 2.2 * ** * 2.0 * ** * 1.7 ** ** * Relative 1.5 ** ** * Entropy 1.2 ** ** * (13.6 bits) 1.0 ***** * 0.7 ******* 0.5 ******** 0.2 ******** 0.0 -------- Multilevel GGGTGGGG consensus T G C sequence T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif KGGTGGSG MEME-5 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr3L:17001182-17001302 26 2.28e-06 CCGTCTCAGT GGGTGGGG CTGGTCTAAA chr3L:3209067-3209187 34 7.57e-06 GAACTTGATA TGGTGGGG GCTACTACGA chr3R:13819187-13819307 41 7.57e-06 GAAGGAGAGC TGGTGGGG TGGCGCAGCA chr2L:10849704-10849824 109 7.57e-06 TCGGGGGGAT TGGTGGGG GGAA chr3R:7076720-7076840 36 7.57e-06 GATTTGCCAG TGGTGGGG TGATGTCGGA chr2R:24749560-24749680 57 9.82e-06 CTTGACGAAT GGGTGGCG ATAAGCCGCA chr3R:9503787-9503907 107 1.21e-05 CAGCGAATCA TGGGGGGG AGGACT chr3L:17401052-17401172 112 1.21e-05 ACCCCCCTTT TGGGGGGG C chr2R:24963337-24963457 93 2.35e-05 AGTGCTGAAG GGGTGGTG GTTTGGTGGG chr2L:20431342-20431462 105 2.35e-05 CTCGTACTCT GGGTGGTG GTACTCTA chr2R:19373817-19373937 48 2.75e-05 AAAGGGGGGC AGGTGGGG TGTATGCCTG chr3R:9946576-9946696 102 3.20e-05 CACCGAGTGC GGGGGGTG AGGGGACTAA chrX:16890727-16890847 55 4.24e-05 TGGCCTGATT TGGTGGTG TTTGCTCGGC chr2R:10045462-10045582 57 5.42e-05 GAAACGAAAA AGGTGGCG TGATCGGTAT chr2L:7968312-7968432 70 5.64e-05 GGTTATTGCC GGCTGGCG TTGTTTCTAT chr3L:21636729-21636849 70 6.09e-05 GGCGGTAAAA TGCGGGGG ATGGGCAATC chr3R:21522352-21522472 96 6.09e-05 TGTTTTATTC AGGGGGCG TACGCTAATC chr2L:5618137-5618257 54 6.21e-05 GCTTTTTGTT GGCGGGCG CTTTTCACTT chr2L:7775394-7775514 108 6.82e-05 GATGACAACG GCGTGGGG ATTGC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif KGGTGGSG MEME-5 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr3L:17001182-17001302 2.3e-06 25_[+5]_87 chr3L:3209067-3209187 7.6e-06 33_[+5]_79 chr3R:13819187-13819307 7.6e-06 40_[+5]_72 chr2L:10849704-10849824 7.6e-06 108_[+5]_4 chr3R:7076720-7076840 7.6e-06 35_[+5]_77 chr2R:24749560-24749680 9.8e-06 56_[+5]_56 chr3R:9503787-9503907 1.2e-05 106_[+5]_6 chr3L:17401052-17401172 1.2e-05 111_[+5]_1 chr2R:24963337-24963457 2.4e-05 92_[+5]_20 chr2L:20431342-20431462 2.4e-05 104_[+5]_8 chr2R:19373817-19373937 2.7e-05 47_[+5]_65 chr3R:9946576-9946696 3.2e-05 101_[+5]_11 chrX:16890727-16890847 4.2e-05 54_[+5]_58 chr2R:10045462-10045582 5.4e-05 56_[+5]_56 chr2L:7968312-7968432 5.6e-05 69_[+5]_43 chr3L:21636729-21636849 6.1e-05 69_[+5]_43 chr3R:21522352-21522472 6.1e-05 95_[+5]_17 chr2L:5618137-5618257 6.2e-05 53_[+5]_59 chr2L:7775394-7775514 6.8e-05 107_[+5]_5 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif KGGTGGSG MEME-5 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF KGGTGGSG width=8 seqs=19 chr3L:17001182-17001302 ( 26) GGGTGGGG 1 chr3L:3209067-3209187 ( 34) TGGTGGGG 1 chr3R:13819187-13819307 ( 41) TGGTGGGG 1 chr2L:10849704-10849824 ( 109) TGGTGGGG 1 chr3R:7076720-7076840 ( 36) TGGTGGGG 1 chr2R:24749560-24749680 ( 57) GGGTGGCG 1 chr3R:9503787-9503907 ( 107) TGGGGGGG 1 chr3L:17401052-17401172 ( 112) TGGGGGGG 1 chr2R:24963337-24963457 ( 93) GGGTGGTG 1 chr2L:20431342-20431462 ( 105) GGGTGGTG 1 chr2R:19373817-19373937 ( 48) AGGTGGGG 1 chr3R:9946576-9946696 ( 102) GGGGGGTG 1 chrX:16890727-16890847 ( 55) TGGTGGTG 1 chr2R:10045462-10045582 ( 57) AGGTGGCG 1 chr2L:7968312-7968432 ( 70) GGCTGGCG 1 chr3L:21636729-21636849 ( 70) TGCGGGGG 1 chr3R:21522352-21522472 ( 96) AGGGGGCG 1 chr2L:5618137-5618257 ( 54) GGCGGGCG 1 chr2L:7775394-7775514 ( 108) GCGTGGGG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif KGGTGGSG MEME-5 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 28250 bayes= 11.4349 E= 1.5e+004 -100 -1089 120 40 -1089 -178 237 -1089 -1089 -19 220 -1089 -1089 -1089 78 110 -1089 -1089 244 -1089 -1089 -1089 244 -1089 -1089 54 152 -60 -1089 -1089 244 -1089 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif KGGTGGSG MEME-5 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 19 E= 1.5e+004 0.157895 0.000000 0.421053 0.421053 0.000000 0.052632 0.947368 0.000000 0.000000 0.157895 0.842105 0.000000 0.000000 0.000000 0.315789 0.684211 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.263158 0.526316 0.210526 0.000000 0.000000 1.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif KGGTGGSG MEME-5 regular expression -------------------------------------------------------------------------------- [GT]GG[TG]GG[GCT]G -------------------------------------------------------------------------------- Time 32.72 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr2L:4930704-4930824 4.71e-01 120 chr3L:19499485-19499605 3.93e-03 25_[+1(6.96e-05)]_87 chr2L:1086617-1086737 4.73e-01 120 chr3L:17401052-17401172 1.63e-05 99_[+1(3.18e-06)]_4_[+5(1.21e-05)]_\ 1 chr2R:17271363-17271483 9.80e-01 120 chr3L:12050046-12050166 2.14e-02 120 chr3R:18546330-18546450 1.32e-01 2_[+4(4.96e-05)]_110 chr2L:13088628-13088748 2.04e-01 120 chr3R:30913838-30913958 4.63e-02 120 chr2L:8385157-8385277 1.65e-01 83_[+3(6.08e-05)]_29 chr3L:5247201-5247321 3.34e-01 120 chr3R:26248241-26248361 9.83e-01 120 chr3L:3772370-3772490 5.94e-01 120 chr3L:11593857-11593977 9.63e-01 120 chr2R:21236777-21236897 6.02e-02 120 chr2L:8619632-8619752 1.09e-02 82_[+3(1.48e-05)]_30 chr3R:7076720-7076840 3.39e-03 35_[+5(7.57e-06)]_77 chr3L:4663914-4664034 7.92e-01 120 chr3R:17774643-17774763 2.65e-01 12_[+4(3.06e-05)]_100 chr3L:11599423-11599543 1.47e-01 120 chr3R:15402780-15402900 2.24e-01 120 chr3R:21522352-21522472 1.14e-02 95_[+5(6.09e-05)]_17 chr2L:18713871-18713991 5.11e-03 71_[+4(3.06e-05)]_21_[+3(7.43e-05)]_\ 12 chr3L:3187312-3187432 1.44e-01 120 chr2L:1135605-1135725 1.07e-01 86_[+3(7.43e-05)]_26 chr3R:20545852-20545972 2.53e-02 27_[+4(3.06e-05)]_85 chrX:12778180-12778300 1.56e-01 120 chr3R:28025357-28025477 1.65e-01 120 chr2R:13293873-13293993 3.41e-04 65_[+2(1.15e-05)]_47 chr2L:13156491-13156611 1.00e+00 120 chr3L:2426526-2426646 1.15e-01 120 chr2L:9754937-9755057 4.88e-01 120 chr2L:14398712-14398832 3.70e-01 120 chr3L:8985254-8985374 3.88e-02 120 chr3L:21846762-21846882 7.28e-02 106_[+2(6.19e-05)]_6 chr3L:10504783-10504903 1.00e+00 120 chr2R:21649109-21649229 1.41e-03 4_[+4(3.06e-05)]_108 chr3R:10330487-10330607 2.26e-02 39_[+4(1.11e-05)]_73 chr3L:10110467-10110587 2.07e-01 67_[+4(4.96e-05)]_45 chr3L:20884121-20884241 8.54e-01 120 chr3R:30084202-30084322 7.85e-01 120 chrX:2108745-2108865 5.96e-01 120 chr2L:7775394-7775514 3.70e-02 107_[+5(6.82e-05)]_5 chr3R:31306580-31306700 5.18e-01 120 chr3L:21909021-21909141 2.41e-01 120 chr2R:7155825-7155945 8.01e-01 120 chr3R:4694972-4695092 2.07e-01 120 chr2L:16672406-16672526 6.39e-01 120 chr3L:19504829-19504949 2.01e-01 120 chr3R:18578095-18578215 9.22e-01 120 chr3R:30905682-30905802 1.31e-02 120 chr3L:22053469-22053589 9.87e-03 90_[+2(4.15e-05)]_22 chr2L:8233784-8233904 8.84e-01 120 chr3R:23159725-23159845 3.13e-01 120 chr2L:14501770-14501890 7.06e-01 120 chrX:21010699-21010819 9.76e-02 120 chr2R:21409744-21409864 9.65e-01 120 chr3L:14819376-14819496 7.71e-01 120 chrX:11730152-11730272 9.75e-01 120 chr2R:12186210-12186330 2.97e-01 120 chr3L:5639794-5639914 9.86e-05 74_[+2(1.79e-05)]_18_[+1(3.18e-06)]_\ 12 chr3R:13714243-13714363 6.67e-02 120 chr3L:12074002-12074122 9.83e-01 120 chr3L:17257334-17257454 9.82e-01 120 chr3R:7217310-7217430 7.78e-01 120 chr2L:5117209-5117329 9.55e-01 120 chr3R:17910357-17910477 5.69e-01 120 chr3L:9193123-9193243 6.80e-01 120 chr2R:10799775-10799895 1.56e-02 120 chr3L:9361958-9362078 9.24e-01 120 chr3R:12688228-12688348 1.79e-03 89_[+1(7.57e-06)]_23 chr2L:9735488-9735608 8.22e-01 120 chr3L:16644042-16644162 8.82e-01 120 chr2R:20314858-20314978 1.20e-02 120 chr2L:7968111-7968231 8.84e-01 120 chr3R:26260971-26261091 1.38e-03 45_[+1(1.44e-05)]_67 chrX:16569528-16569648 2.96e-03 87_[+3(8.75e-05)]_25 chr3L:20353797-20353917 7.53e-01 120 chr3L:7835660-7835780 9.72e-01 120 chr2R:24747690-24747810 8.14e-01 120 chr2L:22108793-22108913 3.79e-03 57_[+1(3.18e-06)]_55 chr3R:21195690-21195810 8.67e-01 120 chr3L:9421172-9421292 7.24e-01 120 chr2R:9184552-9184672 9.98e-01 120 chr2L:5303052-5303172 8.97e-01 120 chr3R:23667749-23667869 9.78e-01 120 chr2L:18985912-18986032 2.72e-01 120 chr2L:5890071-5890191 5.42e-01 120 chr2R:6993956-6994076 8.24e-02 54_[+4(3.06e-05)]_58 chrX:13345471-13345591 9.03e-01 120 chr3R:4706190-4706310 3.55e-01 120 chr2R:16620776-16620896 9.29e-01 120 chr2R:19461664-19461784 1.39e-01 120 chr2L:18153235-18153355 6.12e-01 120 chrX:13105375-13105495 1.36e-01 24_[+2(7.98e-05)]_88 chr2L:5302397-5302517 4.16e-01 120 chr2R:10395586-10395706 2.42e-02 111_[+2(7.61e-05)]_1 chrX:16890727-16890847 1.32e-02 54_[+5(4.24e-05)]_58 chr3L:7833354-7833474 9.83e-01 120 chr3L:5643024-5643144 5.82e-01 120 chr2R:15304849-15304969 7.88e-02 [+1(6.96e-05)]_112 chr3R:21588272-21588392 1.49e-02 61_[+4(3.06e-05)]_51 chrX:4691357-4691477 5.81e-01 120 chrX:2635197-2635317 2.15e-01 120 chr2R:10136174-10136294 8.65e-01 120 chr2L:13207222-13207342 2.23e-03 71_[+3(1.48e-05)]_41 chr3L:17603681-17603801 1.30e-01 120 chr3R:21823178-21823298 1.66e-02 42_[+2(3.61e-06)]_70 chr3L:8447933-8448053 3.95e-02 42_[+4(1.11e-05)]_70 chr3L:14381706-14381826 7.26e-01 120 chr3L:5641719-5641839 1.26e-04 85_[+1(3.18e-06)]_27 chr3L:17814164-17814284 3.37e-01 120 chr3R:12398221-12398341 6.80e-02 120 chr3R:30454354-30454474 2.82e-02 65_[+2(2.16e-05)]_47 chr3R:9503787-9503907 3.36e-02 106_[+5(1.21e-05)]_6 chr3R:10330808-10330928 1.00e-01 90_[+2(7.23e-05)]_22 chr2L:6080513-6080633 1.81e-03 42_[+1(1.32e-05)]_70 chr3R:9946576-9946696 6.88e-06 17_[+4(4.96e-05)]_44_[+3(1.48e-05)]_\ 24_[+5(3.20e-05)]_11 chr3R:18438330-18438450 2.20e-03 72_[+4(6.88e-05)]_40 chr3L:8979170-8979290 9.59e-01 120 chr2L:3059329-3059449 6.93e-03 120 chr3R:26987643-26987763 8.55e-01 120 chr2R:9830278-9830398 5.81e-01 120 chr3R:25268432-25268552 2.69e-01 120 chr2L:19415952-19416072 1.00e+00 120 chr2R:10045462-10045582 9.30e-03 56_[+5(5.42e-05)]_56 chr3L:9503959-9504079 6.58e-01 120 chr3L:19496085-19496205 6.93e-03 120 chr2L:5618137-5618257 1.65e-01 53_[+5(6.21e-05)]_59 chr3R:10111702-10111822 9.55e-01 120 chr2R:8120588-8120708 2.78e-02 79_[+4(6.88e-05)]_33 chrX:21519358-21519478 5.21e-02 51_[+1(4.51e-05)]_61 chr2R:19373817-19373937 2.17e-02 47_[+5(2.75e-05)]_65 chr2L:13461018-13461138 9.76e-01 120 chr3R:5839099-5839219 2.31e-03 120 chr3L:9398554-9398674 1.11e-01 120 chr3L:8453919-8454039 9.76e-01 120 chr3R:10679262-10679382 7.25e-01 120 chr3R:25280113-25280233 5.88e-02 30_[+4(1.11e-05)]_82 chr3R:15366994-15367114 8.92e-01 120 chr2L:20431342-20431462 8.94e-04 104_[+5(2.35e-05)]_8 chr3L:16804758-16804878 3.07e-01 120 chr2R:15846374-15846494 4.94e-01 120 chr3L:2800418-2800538 9.64e-01 120 chr2L:9737875-9737995 1.32e-01 120 chr2L:13801299-13801419 3.67e-01 120 chr3R:22518420-22518540 5.80e-04 76_[+1(1.76e-05)]_36 chr3L:15996940-15997060 9.80e-01 120 chr2L:1048578-1048698 4.81e-01 120 chr3R:14217960-14218080 9.53e-01 120 chr2L:3507601-3507721 9.83e-01 120 chr2L:14336601-14336721 1.95e-01 120 chr2L:18548925-18549045 5.39e-01 120 chr2R:11423538-11423658 1.35e-02 19_[+3(1.83e-05)]_93 chr2L:9526628-9526748 2.40e-02 120 chr3L:3940706-3940826 1.21e-01 111_[+1(2.52e-05)]_1 chr2R:10553802-10553922 1.29e-02 73_[+3(3.59e-05)]_39 chr2R:23672654-23672774 5.31e-03 66_[+4(6.88e-05)]_46 chr2L:10849704-10849824 6.18e-02 108_[+5(7.57e-06)]_4 chr2L:1731039-1731159 7.36e-01 120 chr2R:7731061-7731181 4.79e-01 120 chr3R:8577744-8577864 1.00e+00 120 chrX:2685335-2685455 7.81e-01 120 chr3R:21193910-21194030 1.43e-01 120 chr3R:22455854-22455974 8.59e-02 90_[+2(1.79e-05)]_22 chr3R:11173261-11173381 9.40e-01 120 chr3R:8654244-8654364 3.53e-02 69_[+4(1.11e-05)]_43 chr3L:17956596-17956716 2.01e-02 103_[+3(1.83e-05)]_9 chr3L:17001182-17001302 4.60e-04 25_[+5(2.28e-06)]_10_[+5(7.57e-06)]_\ 69 chr3R:8712821-8712941 5.40e-03 100_[+2(9.96e-05)]_12 chr3R:27662154-27662274 5.70e-03 120 chr2L:18459804-18459924 8.84e-04 1_[+4(4.96e-05)]_111 chr2L:13206357-13206477 4.29e-02 120 chr3R:13819187-13819307 2.43e-06 40_[+5(7.57e-06)]_1_[+3(3.59e-05)]_\ 22_[+4(3.06e-05)]_33 chr2L:9669487-9669607 9.96e-01 120 chr3L:9065034-9065154 4.79e-01 120 chr3R:10380106-10380226 1.00e+00 120 chr3R:10311699-10311819 9.65e-01 120 chr3R:18169142-18169262 2.47e-01 120 chr3R:11178504-11178624 6.36e-01 120 chr3R:5694577-5694697 9.99e-01 120 chr2L:16530184-16530304 1.91e-02 120 chr3R:26801502-26801622 8.84e-01 120 chr2L:2956458-2956578 7.77e-01 120 chr3R:25855739-25855859 8.95e-01 120 chr3R:21157229-21157349 7.60e-01 120 chr3R:20549075-20549195 1.67e-02 29_[+3(3.59e-05)]_83 chrX:3675690-3675810 2.72e-03 55_[+5(3.60e-06)]_57 chr3R:23067479-23067599 6.71e-01 120 chr2L:18441117-18441237 8.53e-02 120 chr3R:31250583-31250703 1.00e+00 120 chr3L:21321946-21322066 8.06e-01 120 chrX:15313997-15314117 6.63e-01 120 chr3L:3209067-3209187 1.05e-03 33_[+5(7.57e-06)]_79 chr3R:19924414-19924534 6.75e-02 70_[+4(3.06e-05)]_42 chr2R:12279568-12279688 4.61e-04 83_[+2(9.39e-06)]_4_[+3(8.75e-05)]_\ 17 chr3R:26009846-26009966 1.04e-01 120 chr2L:1970817-1970937 1.59e-03 56_[+1(1.32e-05)]_56 chr2L:4417072-4417192 1.33e-01 120 chr2L:5007427-5007547 6.04e-01 120 chr2R:22373587-22373707 6.51e-01 120 chrX:16086217-16086337 1.35e-01 120 chr2L:9010426-9010546 4.10e-01 120 chr3R:26259072-26259192 1.50e-04 76_[+2(1.15e-05)]_36 chr3R:9075035-9075155 9.79e-01 120 chr3L:10756199-10756319 9.73e-01 120 chr3L:12075074-12075194 3.50e-04 31_[+1(4.33e-06)]_81 chr2R:17870044-17870164 5.53e-01 120 chr2L:18632448-18632568 5.67e-01 120 chr3R:23164278-23164398 1.61e-02 120 chrX:3265979-3266099 1.23e-01 120 chr2L:8163882-8164002 1.51e-01 120 chr2L:9459415-9459535 5.11e-03 82_[+3(8.75e-05)]_30 chrX:2107941-2108061 1.83e-01 120 chr3L:2572130-2572250 4.40e-02 79_[+1(3.74e-05)]_33 chr3R:14680518-14680638 6.45e-04 [+2(1.79e-05)]_112 chr3L:11656315-11656435 8.83e-01 120 chr3L:9466603-9466723 9.54e-01 120 chr2L:435575-435695 1.00e+00 120 chr3L:19044935-19045055 9.59e-02 120 chr3R:14285734-14285854 1.79e-02 112_[+2(1.79e-05)] chr3L:21343385-21343505 1.08e-02 7_[+3(4.89e-05)]_105 chr3L:17049907-17050027 9.44e-05 7_[+3(9.87e-06)]_105 chrX:9466265-9466385 7.87e-03 76_[+2(3.19e-05)]_36 chr3L:751939-752059 6.99e-02 57_[+2(4.73e-05)]_55 chr2L:5003159-5003279 9.74e-01 120 chr2L:125509-125629 2.14e-01 120 chr3R:24626344-24626464 9.91e-01 120 chr3R:21931489-21931609 8.52e-01 120 chr3L:17000468-17000588 5.58e-03 120 chr3R:9430498-9430618 4.77e-01 120 chr3L:5359428-5359548 1.28e-01 120 chr3R:15898469-15898589 9.95e-01 120 chr3L:5807517-5807637 1.28e-03 47_[+3(3.40e-06)]_65 chrX:11146949-11147069 2.03e-03 10_[+3(4.89e-05)]_102 chr3L:21636729-21636849 3.43e-02 69_[+5(6.09e-05)]_43 chr2R:24963337-24963457 1.69e-02 92_[+5(2.35e-05)]_20 chr3R:12442608-12442728 1.00e+00 120 chr2R:22789381-22789501 1.55e-01 120 chr2R:24749560-24749680 7.16e-03 56_[+5(9.82e-06)]_56 chr3R:30308228-30308348 5.43e-03 13_[+1(3.18e-06)]_99 chr3L:21892343-21892463 8.31e-03 120 chr2L:12002155-12002275 6.29e-02 34_[+2(4.36e-05)]_78 chr2R:17405092-17405212 1.30e-01 120 chr2L:7968312-7968432 9.48e-04 69_[+5(5.64e-05)]_17_[+3(8.75e-05)]_\ 18 chr2L:11736164-11736284 4.97e-02 120 chr2L:13839055-13839175 1.00e+00 120 chr2L:17448566-17448686 2.94e-05 27_[+1(3.18e-06)]_22_[+1(5.41e-05)]_\ 41_[+2(9.39e-06)]_6 chr2R:14073604-14073724 2.15e-06 101_[+2(3.61e-06)]_11 chr2R:10272889-10273009 1.03e-01 30_[+4(3.06e-05)]_82 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (5) found. ******************************************************************************** CPU: c28n05.farnam.hpc.yale.internal ********************************************************************************