******************************************************************************** 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/Hr4.fasta CONTROL SEQUENCES= --none-- ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ chr3R:13831165-13831285 1.0000 120 chr2R:23278846-23278966 1.0000 120 chr3R:24777261-24777381 1.0000 120 chr2L:20296001-20296121 1.0000 120 chr2L:16501521-16501641 1.0000 120 chr3L:7598441-7598561 1.0000 120 chrX:8396723-8396843 1.0000 120 chr2R:23432706-23432826 1.0000 120 chr3R:29982170-29982290 1.0000 120 chr3R:13995535-13995655 1.0000 120 chr3L:6453603-6453723 1.0000 120 chr3R:23638509-23638629 1.0000 120 chr2L:18907564-18907684 1.0000 120 chr2R:23000868-23000988 1.0000 120 chr3L:6997078-6997198 1.0000 120 chr2L:2478492-2478612 1.0000 120 chr2L:19307798-19307918 1.0000 120 chr2L:18725002-18725122 1.0000 120 chr3R:31251465-31251585 1.0000 120 chr2R:17635158-17635278 1.0000 120 chrX:8843896-8844016 1.0000 120 chr2L:8923538-8923658 1.0000 120 chr3L:1392684-1392804 1.0000 120 chr2L:20943309-20943429 1.0000 120 chrX:6912399-6912519 1.0000 120 chr2R:13769541-13769661 1.0000 120 chr3R:9582150-9582270 1.0000 120 chr2L:10748384-10748504 1.0000 120 chr2L:18719698-18719818 1.0000 120 chr3R:24017814-24017934 1.0000 120 chr3R:18624722-18624842 1.0000 120 chr3L:3657005-3657125 1.0000 120 chr3L:1371068-1371188 1.0000 120 chr3L:4736740-4736860 1.0000 120 chr3R:23393656-23393776 1.0000 120 chr2R:14111895-14112015 1.0000 120 chr2L:3635547-3635667 1.0000 120 chr3R:18796353-18796473 1.0000 120 chr3L:3440267-3440387 1.0000 120 chr2L:664462-664582 1.0000 120 chr3R:23416696-23416816 1.0000 120 chr3R:8918916-8919036 1.0000 120 chr3R:31870625-31870745 1.0000 120 chr3L:19011302-19011422 1.0000 120 chr3R:17430590-17430710 1.0000 120 chr2L:18744015-18744135 1.0000 120 chr2L:3482201-3482321 1.0000 120 chr3R:24219225-24219345 1.0000 120 chr2R:18901719-18901839 1.0000 120 chr3L:12073233-12073353 1.0000 120 chr2L:7938599-7938719 1.0000 120 chr3L:8641164-8641284 1.0000 120 chr3L:6263690-6263810 1.0000 120 chr3R:23527550-23527670 1.0000 120 chr2R:7905141-7905261 1.0000 120 chrX:4264428-4264548 1.0000 120 chr3L:7877666-7877786 1.0000 120 chr3R:30343152-30343272 1.0000 120 chr3R:26428371-26428491 1.0000 120 chr2R:20024422-20024542 1.0000 120 chr2L:1073704-1073824 1.0000 120 chr3R:14455587-14455707 1.0000 120 chr3R:23399141-23399261 1.0000 120 chr3R:24886615-24886735 1.0000 120 chrX:10933927-10934047 1.0000 120 chr3R:30329961-30330081 1.0000 120 chr3R:23910590-23910710 1.0000 120 chrX:4965816-4965936 1.0000 120 chr2L:3881313-3881433 1.0000 120 chr2R:11763059-11763179 1.0000 120 chr3R:30163405-30163525 1.0000 120 chr3L:12060270-12060390 1.0000 120 chr3R:23365146-23365266 1.0000 120 chr2R:18301664-18301784 1.0000 120 chr2R:20652432-20652552 1.0000 120 chrX:1979782-1979902 1.0000 120 chr3R:18493928-18494048 1.0000 120 chr3R:31627348-31627468 1.0000 120 chr3R:31443624-31443744 1.0000 120 chr3R:31345738-31345858 1.0000 120 chr3L:21229892-21230012 1.0000 120 chr2L:20960164-20960284 1.0000 120 chrX:13911297-13911417 1.0000 120 chr2R:7118983-7119103 1.0000 120 chr3R:5330491-5330611 1.0000 120 chr3L:3283415-3283535 1.0000 120 chr2R:10216553-10216673 1.0000 120 chr2L:3731198-3731318 1.0000 120 chrX:2220042-2220162 1.0000 120 chr3R:30312669-30312789 1.0000 120 chr3R:6214367-6214487 1.0000 120 chr2L:16803735-16803855 1.0000 120 chr2L:604241-604361 1.0000 120 chr3R:24204158-24204278 1.0000 120 chr3R:31440157-31440277 1.0000 120 chr3R:21731772-21731892 1.0000 120 chrX:13909281-13909401 1.0000 120 chr2L:723057-723177 1.0000 120 chr3L:6268234-6268354 1.0000 120 chrX:10877167-10877287 1.0000 120 chr3R:23407991-23408111 1.0000 120 chrX:3454850-3454970 1.0000 120 chrX:10283978-10284098 1.0000 120 chr2L:14318771-14318891 1.0000 120 chr2L:3428820-3428940 1.0000 120 chr2R:14020696-14020816 1.0000 120 chr3L:6322841-6322961 1.0000 120 chrX:10953396-10953516 1.0000 120 chrX:6303383-6303503 1.0000 120 chr3L:19196748-19196868 1.0000 120 chr3L:2795675-2795795 1.0000 120 chr3L:19329633-19329753 1.0000 120 chr3R:21703503-21703623 1.0000 120 chrX:1988827-1988947 1.0000 120 chrX:1979134-1979254 1.0000 120 chr3L:741850-741970 1.0000 120 chr3R:31243211-31243331 1.0000 120 chr3R:10283241-10283361 1.0000 120 chr3L:6978219-6978339 1.0000 120 chr3R:15541065-15541185 1.0000 120 chrX:11492345-11492465 1.0000 120 chr2R:23020501-23020621 1.0000 120 chr3L:564137-564257 1.0000 120 chr3R:14720224-14720344 1.0000 120 chr2L:20844531-20844651 1.0000 120 chr2R:18588973-18589093 1.0000 120 chr2R:23761503-23761623 1.0000 120 chr2L:7949186-7949306 1.0000 120 chr3L:11155550-11155670 1.0000 120 chr3R:9924600-9924720 1.0000 120 chr2L:18331766-18331886 1.0000 120 chr2R:17407718-17407838 1.0000 120 chr2R:22119844-22119964 1.0000 120 chr2R:9024647-9024767 1.0000 120 chrX:7579164-7579284 1.0000 120 chr2R:8646544-8646664 1.0000 120 chr3R:14009763-14009883 1.0000 120 chr2L:712409-712529 1.0000 120 chr3R:23737801-23737921 1.0000 120 chrX:17274952-17275072 1.0000 120 chr3L:3772751-3772871 1.0000 120 chr3L:3649631-3649751 1.0000 120 chr3R:29847261-29847381 1.0000 120 chr3R:22150099-22150219 1.0000 120 chr2R:13768456-13768576 1.0000 120 chr3R:14761211-14761331 1.0000 120 chr3R:24910242-24910362 1.0000 120 chrX:3423524-3423644 1.0000 120 chr3R:28850763-28850883 1.0000 120 chr3L:6331818-6331938 1.0000 120 chr3R:25051591-25051711 1.0000 120 chr2L:20716862-20716982 1.0000 120 chr3R:26479378-26479498 1.0000 120 chr3L:6307436-6307556 1.0000 120 chr2R:18300302-18300422 1.0000 120 chr3R:29450508-29450628 1.0000 120 chr3L:756504-756624 1.0000 120 chr2L:7918914-7919034 1.0000 120 chr2R:18893733-18893853 1.0000 120 chr3R:30872849-30872969 1.0000 120 chrX:2503554-2503674 1.0000 120 chr3L:1844750-1844870 1.0000 120 chr3L:16892873-16892993 1.0000 120 chr3R:8234028-8234148 1.0000 120 chr3L:19326189-19326309 1.0000 120 chr2R:16742187-16742307 1.0000 120 chr3L:3419719-3419839 1.0000 120 chr2R:12238135-12238255 1.0000 120 chr3R:21733090-21733210 1.0000 120 chr3L:8319255-8319375 1.0000 120 chrX:3696686-3696806 1.0000 120 chr3L:7147928-7148048 1.0000 120 chr3R:19996526-19996646 1.0000 120 chrX:9653407-9653527 1.0000 120 chr3L:8782112-8782232 1.0000 120 chr3R:24908199-24908319 1.0000 120 chrX:10536105-10536225 1.0000 120 chr3R:12297380-12297500 1.0000 120 chr2R:12229671-12229791 1.0000 120 chr3L:5385943-5386063 1.0000 120 chr2L:9618059-9618179 1.0000 120 chr3L:10444098-10444218 1.0000 120 chr2R:7282255-7282375 1.0000 120 chr3R:19808249-19808369 1.0000 120 chr2R:8645855-8645975 1.0000 120 chr3L:4393004-4393124 1.0000 120 chr3L:1900780-1900900 1.0000 120 chr2R:8358049-8358169 1.0000 120 chr2R:7744737-7744857 1.0000 120 chrX:3453570-3453690 1.0000 120 chr3L:7632972-7633092 1.0000 120 chr3L:8422344-8422464 1.0000 120 chr3R:23395830-23395950 1.0000 120 chr3R:22668780-22668900 1.0000 120 chr2R:7173181-7173301 1.0000 120 chr2R:18899124-18899244 1.0000 120 chr3L:20610604-20610724 1.0000 120 chr3R:31767672-31767792 1.0000 120 chr2L:18752181-18752301 1.0000 120 chr2L:7073214-7073334 1.0000 120 chrX:20130568-20130688 1.0000 120 chr3R:31319960-31320080 1.0000 120 chr2L:5495102-5495222 1.0000 120 chr3L:13180490-13180610 1.0000 120 chr2R:14326147-14326267 1.0000 120 chr2L:20328091-20328211 1.0000 120 chr3R:29757888-29758008 1.0000 120 chr3R:14280439-14280559 1.0000 120 chr3L:2145197-2145317 1.0000 120 chr3L:2582446-2582566 1.0000 120 chr2R:22148111-22148231 1.0000 120 chr3R:23417795-23417915 1.0000 120 chr3L:4509189-4509309 1.0000 120 chr3R:22594369-22594489 1.0000 120 chr3R:5324279-5324399 1.0000 120 chrX:17914633-17914753 1.0000 120 chr3R:9420977-9421097 1.0000 120 chr3L:17981254-17981374 1.0000 120 chr2R:18243970-18244090 1.0000 120 chr3R:23391051-23391171 1.0000 120 chr3R:23324120-23324240 1.0000 120 chr2L:1926049-1926169 1.0000 120 chr2L:18005641-18005761 1.0000 120 chr3L:793857-793977 1.0000 120 chr3L:1905385-1905505 1.0000 120 chr2L:15466066-15466186 1.0000 120 chr3R:15425756-15425876 1.0000 120 chrX:22509190-22509310 1.0000 120 chr3L:13451703-13451823 1.0000 120 chr2R:10216752-10216872 1.0000 120 chr2R:14345517-14345637 1.0000 120 chr3R:22727995-22728115 1.0000 120 chr2R:24746571-24746691 1.0000 120 chr3R:30344634-30344754 1.0000 120 chr3R:13952429-13952549 1.0000 120 chr3L:8384121-8384241 1.0000 120 chr3L:16002232-16002352 1.0000 120 chrX:8521593-8521713 1.0000 120 chr3L:16643075-16643195 1.0000 120 chr2L:20340785-20340905 1.0000 120 chr2L:21246845-21246965 1.0000 120 chrX:13238647-13238767 1.0000 120 chr3L:10796109-10796229 1.0000 120 chr3L:14534748-14534868 1.0000 120 chr2L:20002171-20002291 1.0000 120 chr3L:787778-787898 1.0000 120 chr3L:6084584-6084704 1.0000 120 chrX:3740435-3740555 1.0000 120 chr3R:26462845-26462965 1.0000 120 chr3L:11448494-11448614 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_Hr4/ -dna -nmotifs 5 -w 8 -maxsize 250000 -nostatus ../result/final_prediction/fly/fasta/RankLinear8.0_60/Hr4.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 0.344 C 0.155 G 0.152 T 0.35 Background letter frequencies (from file dataset with add-one prior applied): A 0.343 C 0.155 G 0.152 T 0.35 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF CACAGTGC MEME-1 width = 8 sites = 14 llr = 147 E-value = 7.7e+000 ******************************************************************************** -------------------------------------------------------------------------------- Motif CACAGTGC MEME-1 Description -------------------------------------------------------------------------------- Simplified A :6:8:::: pos.-specific C a2a::::7 probability G :1:1a:a3 matrix T :1:1:a:: bits 2.7 * * * * 2.4 * * * * 2.2 * * * * 1.9 * * * ** Relative 1.6 * * **** Entropy 1.4 * * **** (15.2 bits) 1.1 * * **** 0.8 * * **** 0.5 * ****** 0.3 ******** 0.0 -------- Multilevel CACAGTGC consensus C G sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CACAGTGC MEME-1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr3L:20610604-20610724 107 3.54e-06 TATCGAGTAT CACAGTGC AAATCT chr3L:4393004-4393124 100 3.54e-06 TCTTTCTGTG CACAGTGC CACCTCGAGG chr3R:21733090-21733210 110 5.14e-06 TTATTTTCCT CCCAGTGC ACA chr3R:24204158-24204278 106 5.14e-06 CATTTTTTTC CCCAGTGC ACTGGGT chrX:3453570-3453690 102 6.71e-06 ATTGATTTCT CGCAGTGC AGTCAGCCTT chr3L:1844750-1844870 112 6.71e-06 ACCTTTTTCT CGCAGTGC A chr3R:30344634-30344754 12 1.02e-05 ATGAAAAGCG CACAGTGG AGCCAAAAAT chr3L:6331818-6331938 6 1.02e-05 GCGGG CACAGTGG AAATCATTCA chr3L:3440267-3440387 8 1.02e-05 AGGCAGT CACAGTGG AGAATTATAC chr3L:756504-756624 108 1.18e-05 GATATGCTGC CCCAGTGG TTTTA chrX:10536105-10536225 111 1.49e-05 TCTAATTTTC CACGGTGC AA chr3L:4509189-4509309 89 1.85e-05 TTTTGCACCC CACTGTGC AATGACTTTG chr2R:18588973-18589093 113 1.85e-05 TTTTTTGCCC CACTGTGC chr3L:12073233-12073353 109 2.51e-05 TAATTTTTTT CTCAGTGC AGAT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CACAGTGC MEME-1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr3L:20610604-20610724 3.5e-06 106_[+1]_6 chr3L:4393004-4393124 3.5e-06 99_[+1]_13 chr3R:21733090-21733210 5.1e-06 109_[+1]_3 chr3R:24204158-24204278 5.1e-06 105_[+1]_7 chrX:3453570-3453690 6.7e-06 101_[+1]_11 chr3L:1844750-1844870 6.7e-06 111_[+1]_1 chr3R:30344634-30344754 1e-05 11_[+1]_101 chr3L:6331818-6331938 1e-05 5_[+1]_107 chr3L:3440267-3440387 1e-05 7_[+1]_105 chr3L:756504-756624 1.2e-05 107_[+1]_5 chrX:10536105-10536225 1.5e-05 110_[+1]_2 chr3L:4509189-4509309 1.8e-05 88_[+1]_24 chr2R:18588973-18589093 1.8e-05 112_[+1] chr3L:12073233-12073353 2.5e-05 108_[+1]_4 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CACAGTGC MEME-1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF CACAGTGC width=8 seqs=14 chr3L:20610604-20610724 ( 107) CACAGTGC 1 chr3L:4393004-4393124 ( 100) CACAGTGC 1 chr3R:21733090-21733210 ( 110) CCCAGTGC 1 chr3R:24204158-24204278 ( 106) CCCAGTGC 1 chrX:3453570-3453690 ( 102) CGCAGTGC 1 chr3L:1844750-1844870 ( 112) CGCAGTGC 1 chr3R:30344634-30344754 ( 12) CACAGTGG 1 chr3L:6331818-6331938 ( 6) CACAGTGG 1 chr3L:3440267-3440387 ( 8) CACAGTGG 1 chr3L:756504-756624 ( 108) CCCAGTGG 1 chrX:10536105-10536225 ( 111) CACGGTGC 1 chr3L:4509189-4509309 ( 89) CACTGTGC 1 chr2R:18588973-18589093 ( 113) CACTGTGC 1 chr3L:12073233-12073353 ( 109) CTCAGTGC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CACAGTGC MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 28250 bayes= 11.5839 E= 7.7e+000 -1045 269 -1045 -1045 73 47 -9 -229 -1045 269 -1045 -1045 119 -1045 -108 -129 -1045 -1045 272 -1045 -1045 -1045 -1045 152 -1045 -1045 272 -1045 -1045 220 91 -1045 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CACAGTGC MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 14 E= 7.7e+000 0.000000 1.000000 0.000000 0.000000 0.571429 0.214286 0.142857 0.071429 0.000000 1.000000 0.000000 0.000000 0.785714 0.000000 0.071429 0.142857 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 0.714286 0.285714 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CACAGTGC MEME-1 regular expression -------------------------------------------------------------------------------- C[AC]CAGTG[CG] -------------------------------------------------------------------------------- Time 7.74 secs. ******************************************************************************** ******************************************************************************** MOTIF CGAGGCGS MEME-2 width = 8 sites = 2 llr = 27 E-value = 1.0e+004 ******************************************************************************** -------------------------------------------------------------------------------- Motif CGAGGCGS MEME-2 Description -------------------------------------------------------------------------------- Simplified A ::a::::: pos.-specific C a::::a:5 probability G :a:aa:a5 matrix T :::::::: bits 2.7 ** **** 2.4 ** **** 2.2 ** **** 1.9 ** **** Relative 1.6 ******** Entropy 1.4 ******** (19.5 bits) 1.1 ******** 0.8 ******** 0.5 ******** 0.3 ******** 0.0 -------- Multilevel CGAGGCGC consensus G sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CGAGGCGS MEME-2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr3L:4393004-4393124 113 1.35e-06 AGTGCCACCT CGAGGCGC chr2R:14020696-14020816 111 1.35e-06 CCAAGCCAGC CGAGGCGG AG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CGAGGCGS MEME-2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr3L:4393004-4393124 1.4e-06 112_[+2] chr2R:14020696-14020816 1.4e-06 110_[+2]_2 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CGAGGCGS MEME-2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF CGAGGCGS width=8 seqs=2 chr3L:4393004-4393124 ( 113) CGAGGCGC 1 chr2R:14020696-14020816 ( 111) CGAGGCGG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CGAGGCGS MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 28250 bayes= 13.7859 E= 1.0e+004 -765 268 -765 -765 -765 -765 272 -765 154 -765 -765 -765 -765 -765 272 -765 -765 -765 272 -765 -765 268 -765 -765 -765 -765 272 -765 -765 168 172 -765 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CGAGGCGS MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 2 E= 1.0e+004 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.500000 0.500000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CGAGGCGS MEME-2 regular expression -------------------------------------------------------------------------------- CGAGGCG[CG] -------------------------------------------------------------------------------- Time 13.98 secs. ******************************************************************************** ******************************************************************************** MOTIF GGTGCAAG MEME-3 width = 8 sites = 3 llr = 38 E-value = 4.5e+004 ******************************************************************************** -------------------------------------------------------------------------------- Motif GGTGCAAG MEME-3 Description -------------------------------------------------------------------------------- Simplified A :::::aa: pos.-specific C ::::a::: probability G aa:a:::a matrix T ::a::::: bits 2.7 ** ** * 2.4 ** ** * 2.2 ** ** * 1.9 ** ** * Relative 1.6 ******** Entropy 1.4 ******** (18.2 bits) 1.1 ******** 0.8 ******** 0.5 ******** 0.3 ******** 0.0 -------- Multilevel GGTGCAAG consensus sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGTGCAAG MEME-3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr2R:16742187-16742307 69 3.41e-06 GAAAATGTGT GGTGCAAG TTCGAGACCC chr3R:24017814-24017934 44 3.41e-06 GTCACTTCTA GGTGCAAG AAATTAAATC chr2L:20943309-20943429 81 3.41e-06 CATGGCATCC GGTGCAAG TGATAACTTA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGTGCAAG MEME-3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr2R:16742187-16742307 3.4e-06 68_[+3]_44 chr3R:24017814-24017934 3.4e-06 43_[+3]_69 chr2L:20943309-20943429 3.4e-06 80_[+3]_32 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGTGCAAG MEME-3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF GGTGCAAG width=8 seqs=3 chr2R:16742187-16742307 ( 69) GGTGCAAG 1 chr3R:24017814-24017934 ( 44) GGTGCAAG 1 chr2L:20943309-20943429 ( 81) GGTGCAAG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGTGCAAG MEME-3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 28250 bayes= 12.8598 E= 4.5e+004 -823 -823 272 -823 -823 -823 272 -823 -823 -823 -823 151 -823 -823 272 -823 -823 268 -823 -823 154 -823 -823 -823 154 -823 -823 -823 -823 -823 272 -823 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGTGCAAG MEME-3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 3 E= 4.5e+004 0.000000 0.000000 1.000000 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 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGTGCAAG MEME-3 regular expression -------------------------------------------------------------------------------- GGTGCAAG -------------------------------------------------------------------------------- Time 20.30 secs. ******************************************************************************** ******************************************************************************** MOTIF SCAGCCAC MEME-4 width = 8 sites = 3 llr = 38 E-value = 4.0e+004 ******************************************************************************** -------------------------------------------------------------------------------- Motif SCAGCCAC MEME-4 Description -------------------------------------------------------------------------------- Simplified A ::a:::a: pos.-specific C 3a::aa:a probability G 7::a:::: matrix T :::::::: bits 2.7 * *** * 2.4 * *** * 2.2 * *** * 1.9 ** *** * Relative 1.6 ******** Entropy 1.4 ******** (18.3 bits) 1.1 ******** 0.8 ******** 0.5 ******** 0.3 ******** 0.0 -------- Multilevel GCAGCCAC consensus C sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif SCAGCCAC MEME-4 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chrX:1988827-1988947 16 1.57e-06 TGCCGTACTA GCAGCCAC ATCAGGCGGA chr2R:14020696-14020816 73 1.57e-06 GATTGTTGAG GCAGCCAC ATAATCCACT chr3R:14761211-14761331 23 3.17e-06 AGAGAAAAAA CCAGCCAC TAGCCATTAT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif SCAGCCAC MEME-4 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrX:1988827-1988947 1.6e-06 15_[+4]_97 chr2R:14020696-14020816 1.6e-06 72_[+4]_40 chr3R:14761211-14761331 3.2e-06 22_[+4]_90 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif SCAGCCAC MEME-4 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF SCAGCCAC width=8 seqs=3 chrX:1988827-1988947 ( 16) GCAGCCAC 1 chr2R:14020696-14020816 ( 73) GCAGCCAC 1 chr3R:14761211-14761331 ( 23) CCAGCCAC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif SCAGCCAC MEME-4 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 28250 bayes= 12.8598 E= 4.0e+004 -823 110 213 -823 -823 268 -823 -823 154 -823 -823 -823 -823 -823 272 -823 -823 268 -823 -823 -823 268 -823 -823 154 -823 -823 -823 -823 268 -823 -823 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif SCAGCCAC MEME-4 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 3 E= 4.0e+004 0.000000 0.333333 0.666667 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif SCAGCCAC MEME-4 regular expression -------------------------------------------------------------------------------- [GC]CAGCCAC -------------------------------------------------------------------------------- Time 26.63 secs. ******************************************************************************** ******************************************************************************** MOTIF GGWGCAGC MEME-5 width = 8 sites = 2 llr = 25 E-value = 5.4e+004 ******************************************************************************** -------------------------------------------------------------------------------- Motif GGWGCAGC MEME-5 Description -------------------------------------------------------------------------------- Simplified A ::5::a:: pos.-specific C ::::a::a probability G aa:a::a: matrix T ::5::::: bits 2.7 ** ** ** 2.4 ** ** ** 2.2 ** ** ** 1.9 ** ** ** Relative 1.6 ** ***** Entropy 1.4 ** ***** (18.3 bits) 1.1 ** ***** 0.8 ** ***** 0.5 ******** 0.3 ******** 0.0 -------- Multilevel GGAGCAGC consensus T sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGWGCAGC MEME-5 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr3R:31767672-31767792 29 3.05e-06 AGCCTCTGTG GGAGCAGC TCCAAAAGAT chr3R:23399141-23399261 101 3.05e-06 TATTTTTCTA GGTGCAGC GGTATCGTAT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGWGCAGC MEME-5 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr3R:31767672-31767792 3e-06 28_[+5]_84 chr3R:23399141-23399261 3e-06 100_[+5]_12 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGWGCAGC MEME-5 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF GGWGCAGC width=8 seqs=2 chr3R:31767672-31767792 ( 29) GGAGCAGC 1 chr3R:23399141-23399261 ( 101) GGTGCAGC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGWGCAGC MEME-5 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 28250 bayes= 12.9378 E= 5.4e+004 -765 -765 272 -765 -765 -765 272 -765 54 -765 -765 51 -765 -765 272 -765 -765 268 -765 -765 154 -765 -765 -765 -765 -765 272 -765 -765 268 -765 -765 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGWGCAGC MEME-5 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 2 E= 5.4e+004 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.500000 0.000000 0.000000 0.500000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGWGCAGC MEME-5 regular expression -------------------------------------------------------------------------------- GG[AT]GCAGC -------------------------------------------------------------------------------- Time 32.84 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr3R:13831165-13831285 8.06e-01 120 chr2R:23278846-23278966 9.81e-01 120 chr3R:24777261-24777381 9.87e-01 120 chr2L:20296001-20296121 1.42e-01 120 chr2L:16501521-16501641 5.75e-01 120 chr3L:7598441-7598561 1.59e-01 120 chrX:8396723-8396843 1.76e-01 120 chr2R:23432706-23432826 5.76e-01 120 chr3R:29982170-29982290 5.28e-02 120 chr3R:13995535-13995655 2.22e-01 120 chr3L:6453603-6453723 9.42e-01 120 chr3R:23638509-23638629 8.28e-01 120 chr2L:18907564-18907684 9.99e-01 120 chr2R:23000868-23000988 1.10e-02 120 chr3L:6997078-6997198 8.63e-01 120 chr2L:2478492-2478612 8.75e-01 120 chr2L:19307798-19307918 2.81e-01 120 chr2L:18725002-18725122 6.82e-02 120 chr3R:31251465-31251585 9.27e-01 120 chr2R:17635158-17635278 5.75e-01 120 chrX:8843896-8844016 4.53e-02 120 chr2L:8923538-8923658 9.87e-01 120 chr3L:1392684-1392804 2.65e-02 120 chr2L:20943309-20943429 2.29e-03 80_[+3(3.41e-06)]_32 chrX:6912399-6912519 6.10e-01 120 chr2R:13769541-13769661 2.54e-01 120 chr3R:9582150-9582270 1.71e-01 120 chr2L:10748384-10748504 1.14e-01 120 chr2L:18719698-18719818 5.41e-01 120 chr3R:24017814-24017934 1.10e-03 43_[+3(3.41e-06)]_69 chr3R:18624722-18624842 5.80e-01 120 chr3L:3657005-3657125 4.88e-01 120 chr3L:1371068-1371188 2.24e-02 120 chr3L:4736740-4736860 8.05e-03 38_[+4(6.54e-05)]_74 chr3R:23393656-23393776 7.64e-01 120 chr2R:14111895-14112015 7.80e-01 120 chr2L:3635547-3635667 9.16e-01 120 chr3R:18796353-18796473 7.09e-04 120 chr3L:3440267-3440387 5.66e-03 7_[+1(1.02e-05)]_105 chr2L:664462-664582 3.88e-01 120 chr3R:23416696-23416816 9.99e-01 120 chr3R:8918916-8919036 3.40e-01 120 chr3R:31870625-31870745 8.37e-01 120 chr3L:19011302-19011422 6.93e-01 120 chr3R:17430590-17430710 6.01e-01 120 chr2L:18744015-18744135 3.84e-01 120 chr2L:3482201-3482321 1.11e-01 120 chr3R:24219225-24219345 6.16e-01 120 chr2R:18901719-18901839 1.04e-01 120 chr3L:12073233-12073353 1.29e-02 108_[+1(2.51e-05)]_4 chr2L:7938599-7938719 7.95e-01 120 chr3L:8641164-8641284 1.06e-01 39_[+1(9.05e-05)]_73 chr3L:6263690-6263810 6.33e-01 120 chr3R:23527550-23527670 4.63e-01 120 chr2R:7905141-7905261 4.62e-01 120 chrX:4264428-4264548 9.88e-01 120 chr3L:7877666-7877786 5.84e-01 120 chr3R:30343152-30343272 4.81e-01 120 chr3R:26428371-26428491 4.43e-01 120 chr2R:20024422-20024542 9.99e-01 120 chr2L:1073704-1073824 8.06e-01 120 chr3R:14455587-14455707 9.49e-01 120 chr3R:23399141-23399261 2.03e-05 46_[+3(2.28e-05)]_46_[+5(3.05e-06)]_\ 12 chr3R:24886615-24886735 9.91e-01 120 chrX:10933927-10934047 4.75e-01 120 chr3R:30329961-30330081 1.47e-02 120 chr3R:23910590-23910710 9.27e-01 120 chrX:4965816-4965936 8.13e-01 120 chr2L:3881313-3881433 5.22e-01 120 chr2R:11763059-11763179 9.70e-01 120 chr3R:30163405-30163525 1.79e-01 120 chr3L:12060270-12060390 1.82e-01 120 chr3R:23365146-23365266 7.42e-01 120 chr2R:18301664-18301784 3.30e-01 120 chr2R:20652432-20652552 7.49e-01 120 chrX:1979782-1979902 5.12e-01 120 chr3R:18493928-18494048 7.09e-02 120 chr3R:31627348-31627468 9.87e-01 120 chr3R:31443624-31443744 1.00e+00 120 chr3R:31345738-31345858 9.15e-01 120 chr3L:21229892-21230012 4.03e-01 120 chr2L:20960164-20960284 9.84e-01 120 chrX:13911297-13911417 1.03e-01 120 chr2R:7118983-7119103 4.30e-01 120 chr3R:5330491-5330611 9.15e-01 120 chr3L:3283415-3283535 9.52e-01 120 chr2R:10216553-10216673 6.94e-01 120 chr2L:3731198-3731318 9.98e-01 120 chrX:2220042-2220162 7.20e-01 120 chr3R:30312669-30312789 1.21e-01 120 chr3R:6214367-6214487 1.75e-01 120 chr2L:16803735-16803855 8.74e-01 120 chr2L:604241-604361 4.94e-01 120 chr3R:24204158-24204278 3.06e-03 105_[+1(5.14e-06)]_7 chr3R:31440157-31440277 7.75e-02 120 chr3R:21731772-21731892 6.17e-02 120 chrX:13909281-13909401 9.85e-01 120 chr2L:723057-723177 6.54e-02 21_[+2(5.77e-05)]_91 chr3L:6268234-6268354 3.27e-03 32_[+2(6.99e-06)]_80 chrX:10877167-10877287 9.73e-01 120 chr3R:23407991-23408111 9.85e-01 120 chrX:3454850-3454970 4.65e-03 26_[+4(6.54e-05)]_86 chrX:10283978-10284098 9.12e-01 120 chr2L:14318771-14318891 2.46e-02 120 chr2L:3428820-3428940 9.62e-01 120 chr2R:14020696-14020816 9.97e-08 72_[+4(1.57e-06)]_30_[+2(1.35e-06)]_\ 2 chr3L:6322841-6322961 7.17e-01 120 chrX:10953396-10953516 5.47e-01 120 chrX:6303383-6303503 3.82e-01 120 chr3L:19196748-19196868 7.31e-02 120 chr3L:2795675-2795795 6.31e-01 120 chr3L:19329633-19329753 9.29e-02 120 chr3R:21703503-21703623 5.38e-01 120 chrX:1988827-1988947 1.94e-04 15_[+4(1.57e-06)]_97 chrX:1979134-1979254 5.26e-01 120 chr3L:741850-741970 9.87e-01 120 chr3R:31243211-31243331 6.25e-01 120 chr3R:10283241-10283361 1.00e+00 120 chr3L:6978219-6978339 7.47e-01 120 chr3R:15541065-15541185 5.07e-01 120 chrX:11492345-11492465 4.12e-01 120 chr2R:23020501-23020621 2.87e-01 120 chr3L:564137-564257 4.20e-01 120 chr3R:14720224-14720344 1.02e-02 120 chr2L:20844531-20844651 7.87e-02 120 chr2R:18588973-18589093 1.60e-01 112_[+1(1.85e-05)] chr2R:23761503-23761623 5.75e-01 120 chr2L:7949186-7949306 9.91e-01 120 chr3L:11155550-11155670 4.10e-01 120 chr3R:9924600-9924720 3.19e-01 120 chr2L:18331766-18331886 9.99e-01 120 chr2R:17407718-17407838 7.09e-01 120 chr2R:22119844-22119964 7.87e-01 120 chr2R:9024647-9024767 5.80e-01 120 chrX:7579164-7579284 9.97e-01 120 chr2R:8646544-8646664 9.94e-01 120 chr3R:14009763-14009883 6.23e-01 120 chr2L:712409-712529 5.57e-02 120 chr3R:23737801-23737921 6.47e-01 120 chrX:17274952-17275072 4.78e-01 120 chr3L:3772751-3772871 9.86e-01 120 chr3L:3649631-3649751 8.69e-01 120 chr3R:29847261-29847381 4.57e-03 120 chr3R:22150099-22150219 9.35e-01 120 chr2R:13768456-13768576 3.74e-02 120 chr3R:14761211-14761331 2.87e-03 22_[+4(3.17e-06)]_90 chr3R:24910242-24910362 3.24e-01 120 chrX:3423524-3423644 9.37e-01 120 chr3R:28850763-28850883 9.85e-01 120 chr3L:6331818-6331938 8.36e-03 5_[+1(1.02e-05)]_107 chr3R:25051591-25051711 8.27e-01 120 chr2L:20716862-20716982 7.02e-01 120 chr3R:26479378-26479498 1.83e-01 120 chr3L:6307436-6307556 2.50e-01 120 chr2R:18300302-18300422 2.87e-01 120 chr3R:29450508-29450628 4.64e-01 120 chr3L:756504-756624 5.88e-03 107_[+1(1.18e-05)]_5 chr2L:7918914-7919034 1.00e+00 120 chr2R:18893733-18893853 1.82e-01 102_[+1(4.52e-05)]_10 chr3R:30872849-30872969 1.00e+00 120 chrX:2503554-2503674 8.96e-01 120 chr3L:1844750-1844870 2.50e-02 111_[+1(6.71e-06)]_1 chr3L:16892873-16892993 9.74e-01 120 chr3R:8234028-8234148 9.70e-01 120 chr3L:19326189-19326309 5.81e-01 120 chr2R:16742187-16742307 3.09e-03 68_[+3(3.41e-06)]_44 chr3L:3419719-3419839 1.00e+00 120 chr2R:12238135-12238255 1.00e+00 120 chr3R:21733090-21733210 1.54e-02 109_[+1(5.14e-06)]_3 chr3L:8319255-8319375 9.48e-01 120 chrX:3696686-3696806 6.74e-01 120 chr3L:7147928-7148048 1.52e-01 120 chr3R:19996526-19996646 9.92e-01 120 chrX:9653407-9653527 7.53e-01 120 chr3L:8782112-8782232 7.21e-01 120 chr3R:24908199-24908319 7.74e-01 120 chrX:10536105-10536225 1.54e-02 110_[+1(1.49e-05)]_2 chr3R:12297380-12297500 9.98e-01 120 chr2R:12229671-12229791 8.99e-01 120 chr3L:5385943-5386063 8.56e-01 120 chr2L:9618059-9618179 3.66e-01 120 chr3L:10444098-10444218 5.87e-01 120 chr2R:7282255-7282375 8.59e-01 120 chr3R:19808249-19808369 9.60e-01 120 chr2R:8645855-8645975 6.72e-01 120 chr3L:4393004-4393124 1.15e-05 99_[+1(3.54e-06)]_5_[+2(1.35e-06)] chr3L:1900780-1900900 9.89e-01 120 chr2R:8358049-8358169 7.06e-01 120 chr2R:7744737-7744857 7.75e-01 120 chrX:3453570-3453690 8.03e-04 101_[+1(6.71e-06)]_11 chr3L:7632972-7633092 8.61e-01 120 chr3L:8422344-8422464 9.45e-01 120 chr3R:23395830-23395950 9.98e-01 120 chr3R:22668780-22668900 7.16e-02 120 chr2R:7173181-7173301 2.83e-01 120 chr2R:18899124-18899244 8.39e-01 120 chr3L:20610604-20610724 2.41e-02 106_[+1(3.54e-06)]_6 chr3R:31767672-31767792 1.18e-06 16_[+4(9.18e-06)]_4_[+5(3.05e-06)]_\ 84 chr2L:18752181-18752301 6.21e-01 120 chr2L:7073214-7073334 8.54e-01 120 chrX:20130568-20130688 5.70e-01 120 chr3R:31319960-31320080 8.87e-01 120 chr2L:5495102-5495222 2.45e-01 120 chr3L:13180490-13180610 6.94e-01 120 chr2R:14326147-14326267 4.25e-01 120 chr2L:20328091-20328211 3.09e-01 120 chr3R:29757888-29758008 9.56e-01 120 chr3R:14280439-14280559 6.34e-01 120 chr3L:2145197-2145317 1.14e-01 120 chr3L:2582446-2582566 9.94e-01 120 chr2R:22148111-22148231 2.29e-01 120 chr3R:23417795-23417915 4.05e-01 120 chr3L:4509189-4509309 5.15e-02 88_[+1(1.85e-05)]_24 chr3R:22594369-22594489 6.00e-01 120 chr3R:5324279-5324399 8.85e-02 120 chrX:17914633-17914753 1.92e-01 120 chr3R:9420977-9421097 5.49e-04 120 chr3L:17981254-17981374 1.00e+00 120 chr2R:18243970-18244090 8.40e-01 120 chr3R:23391051-23391171 7.03e-02 120 chr3R:23324120-23324240 2.79e-01 120 chr2L:1926049-1926169 2.91e-01 120 chr2L:18005641-18005761 7.28e-01 120 chr3L:793857-793977 5.13e-01 120 chr3L:1905385-1905505 9.96e-01 120 chr2L:15466066-15466186 4.71e-01 120 chr3R:15425756-15425876 9.57e-01 120 chrX:22509190-22509310 3.97e-01 120 chr3L:13451703-13451823 2.95e-01 120 chr2R:10216752-10216872 3.54e-03 120 chr2R:14345517-14345637 4.66e-01 120 chr3R:22727995-22728115 3.70e-01 120 chr2R:24746571-24746691 4.27e-01 120 chr3R:30344634-30344754 2.82e-03 11_[+1(1.02e-05)]_101 chr3R:13952429-13952549 9.99e-01 120 chr3L:8384121-8384241 4.48e-01 120 chr3L:16002232-16002352 8.06e-01 120 chrX:8521593-8521713 8.05e-01 120 chr3L:16643075-16643195 1.43e-01 120 chr2L:20340785-20340905 6.78e-02 120 chr2L:21246845-21246965 9.07e-01 120 chrX:13238647-13238767 9.98e-01 120 chr3L:10796109-10796229 9.98e-01 120 chr3L:14534748-14534868 8.63e-01 120 chr2L:20002171-20002291 8.75e-01 120 chr3L:787778-787898 8.18e-01 120 chr3L:6084584-6084704 6.34e-01 120 chrX:3740435-3740555 6.63e-01 120 chr3R:26462845-26462965 4.40e-01 120 chr3L:11448494-11448614 7.78e-02 63_[+4(6.54e-05)]_49 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (5) found. ******************************************************************************** CPU: c27n09.farnam.hpc.yale.internal ********************************************************************************