******************************************************************************** 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/fd59A.fasta CONTROL SEQUENCES= --none-- ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ chrX:17355904-17356024 1.0000 120 chr2R:8318257-8318377 1.0000 120 chr2L:612846-612966 1.0000 120 chr2L:1574174-1574294 1.0000 120 chr2L:11966164-11966284 1.0000 120 chr2R:15483166-15483286 1.0000 120 chr3L:18245959-18246079 1.0000 120 chr3L:13288345-13288465 1.0000 120 chr2L:20940899-20941019 1.0000 120 chr2L:18946339-18946459 1.0000 120 chr3R:13851081-13851201 1.0000 120 chr2R:11551109-11551229 1.0000 120 chr3L:12455201-12455321 1.0000 120 chr2R:8995143-8995263 1.0000 120 chr2L:14569418-14569538 1.0000 120 chr3R:7025313-7025433 1.0000 120 chr3R:8107064-8107184 1.0000 120 chr2R:7848711-7848831 1.0000 120 chr3R:28999145-28999265 1.0000 120 chr3L:13178305-13178425 1.0000 120 chr3L:20988037-20988157 1.0000 120 chr2L:5288351-5288471 1.0000 120 chr2R:9498769-9498889 1.0000 120 chr3R:27175904-27176024 1.0000 120 chr3L:14464671-14464791 1.0000 120 chr2L:19156629-19156749 1.0000 120 chr2R:8595873-8595993 1.0000 120 chr2L:3351978-3352098 1.0000 120 chrX:9787540-9787660 1.0000 120 chr3L:16209173-16209293 1.0000 120 chr2R:15047009-15047129 1.0000 120 chr3L:8813626-8813746 1.0000 120 chrX:17351682-17351802 1.0000 120 chr2R:6515157-6515277 1.0000 120 chr2L:3154938-3155058 1.0000 120 chr3L:3338210-3338330 1.0000 120 chr2L:15388397-15388517 1.0000 120 chrX:18537527-18537647 1.0000 120 chr3L:17577048-17577168 1.0000 120 chr3R:30101055-30101175 1.0000 120 chr3R:24496221-24496341 1.0000 120 chr2L:7911471-7911591 1.0000 120 chr3L:13066312-13066432 1.0000 120 chr2R:15000507-15000627 1.0000 120 chr2L:20936595-20936715 1.0000 120 chr3R:10177030-10177150 1.0000 120 chrX:6704079-6704199 1.0000 120 chr3L:8822394-8822514 1.0000 120 chr3L:3109487-3109607 1.0000 120 chr3R:10829938-10830058 1.0000 120 chr3R:6102517-6102637 1.0000 120 chrX:2880826-2880946 1.0000 120 chr2R:20578614-20578734 1.0000 120 chr2L:14572185-14572305 1.0000 120 chr3R:21653043-21653163 1.0000 120 chr2L:1312441-1312561 1.0000 120 chr2L:12840525-12840645 1.0000 120 chr3L:14063556-14063676 1.0000 120 chr3L:16484870-16484990 1.0000 120 chr3L:485054-485174 1.0000 120 chr3L:15220535-15220655 1.0000 120 chr2R:11083884-11084004 1.0000 120 chrX:8800493-8800613 1.0000 120 chr3L:16941454-16941574 1.0000 120 chr2L:2485421-2485541 1.0000 120 chr3R:29091755-29091875 1.0000 120 chr2L:3562503-3562623 1.0000 120 chr3R:29011229-29011349 1.0000 120 chr2L:9736181-9736301 1.0000 120 chr3R:24953291-24953411 1.0000 120 chr2L:2484263-2484383 1.0000 120 chrX:19843015-19843135 1.0000 120 chr2L:1455636-1455756 1.0000 120 chrX:379702-379822 1.0000 120 chr3R:21940271-21940391 1.0000 120 chr3R:30259743-30259863 1.0000 120 chr3R:13846012-13846132 1.0000 120 chr3R:19070633-19070753 1.0000 120 chrX:14134093-14134213 1.0000 120 chr2R:22119894-22120014 1.0000 120 chr3R:24970764-24970884 1.0000 120 chr2L:5372652-5372772 1.0000 120 chr3L:18406043-18406163 1.0000 120 chr2L:20989586-20989706 1.0000 120 chr3L:1711364-1711484 1.0000 120 chr3L:14350986-14351106 1.0000 120 chr3L:21721027-21721147 1.0000 120 chr2L:14665105-14665225 1.0000 120 chr3R:30264988-30265108 1.0000 120 chr2L:2073052-2073172 1.0000 120 chr2L:11399665-11399785 1.0000 120 chr3L:6355190-6355310 1.0000 120 chr3L:21043977-21044097 1.0000 120 chr2L:14529392-14529512 1.0000 120 chr2L:11069683-11069803 1.0000 120 chr2L:646654-646774 1.0000 120 chr3R:6106826-6106946 1.0000 120 chrX:17112110-17112230 1.0000 120 chr3R:13916689-13916809 1.0000 120 chr2L:3557595-3557715 1.0000 120 chr3L:20592702-20592822 1.0000 120 chr2R:21300866-21300986 1.0000 120 chrX:5301036-5301156 1.0000 120 chr3R:21826297-21826417 1.0000 120 chr3L:8284854-8284974 1.0000 120 chrX:7222251-7222371 1.0000 120 chrX:6778240-6778360 1.0000 120 chr3L:18078841-18078961 1.0000 120 chr3R:29847243-29847363 1.0000 120 chr2R:18746909-18747029 1.0000 120 chrX:2358341-2358461 1.0000 120 chr2R:8749912-8750032 1.0000 120 chr3L:16259751-16259871 1.0000 120 chrX:8747802-8747922 1.0000 120 chr3R:5053072-5053192 1.0000 120 chr3L:3106279-3106399 1.0000 120 chrX:4442675-4442795 1.0000 120 chr3R:16210873-16210993 1.0000 120 chr3R:30256364-30256484 1.0000 120 chr2L:3719614-3719734 1.0000 120 chr2R:11048106-11048226 1.0000 120 chr3L:15005910-15006030 1.0000 120 chr2R:21495518-21495638 1.0000 120 chr2R:18271189-18271309 1.0000 120 chr3R:14717353-14717473 1.0000 120 chr2R:19964416-19964536 1.0000 120 chr3L:10562399-10562519 1.0000 120 chr3L:4747518-4747638 1.0000 120 chrX:20482942-20483062 1.0000 120 chr3R:31319923-31320043 1.0000 120 chr3L:20582530-20582650 1.0000 120 chr3L:10913297-10913417 1.0000 120 chr3L:11382764-11382884 1.0000 120 chrX:14017549-14017669 1.0000 120 chr2R:21706440-21706560 1.0000 120 chr3R:8958435-8958555 1.0000 120 chrX:12511422-12511542 1.0000 120 chr3R:27222091-27222211 1.0000 120 chrX:9468445-9468565 1.0000 120 chr2L:5494021-5494141 1.0000 120 chr2R:21224995-21225115 1.0000 120 chr3R:10533296-10533416 1.0000 120 chr3L:10387674-10387794 1.0000 120 chr3R:9346661-9346781 1.0000 120 chr3R:5042552-5042672 1.0000 120 chr2R:23014898-23015018 1.0000 120 chr3L:3073678-3073798 1.0000 120 chr2L:1409831-1409951 1.0000 120 chr2R:13461339-13461459 1.0000 120 chr2L:11074082-11074202 1.0000 120 chr2L:11386494-11386614 1.0000 120 chr3L:19961924-19962044 1.0000 120 chr2L:21847459-21847579 1.0000 120 chr2L:3582803-3582923 1.0000 120 chr3L:10968817-10968937 1.0000 120 chr2R:11033725-11033845 1.0000 120 chr3R:27199541-27199661 1.0000 120 chr2R:21847831-21847951 1.0000 120 chr2L:15909387-15909507 1.0000 120 chr2R:11544153-11544273 1.0000 120 chr3R:14389435-14389555 1.0000 120 chrX:5020191-5020311 1.0000 120 chr2L:8919786-8919906 1.0000 120 chr2R:7912153-7912273 1.0000 120 chr2L:19454518-19454638 1.0000 120 chr3R:18998457-18998577 1.0000 120 chr3L:8013453-8013573 1.0000 120 chr2L:1456999-1457119 1.0000 120 chr3R:27179112-27179232 1.0000 120 chr2R:18567346-18567466 1.0000 120 chr3R:22184230-22184350 1.0000 120 chr3L:22743081-22743201 1.0000 120 chr3R:18485369-18485489 1.0000 120 chr2L:18517131-18517251 1.0000 120 chrX:8215614-8215734 1.0000 120 chr3L:21042714-21042834 1.0000 120 chrX:18929537-18929657 1.0000 120 chrX:18540311-18540431 1.0000 120 chr2L:4069653-4069773 1.0000 120 chr2L:4071679-4071799 1.0000 120 chr2L:5479238-5479358 1.0000 120 chr3R:24143955-24144075 1.0000 120 chr2R:11749467-11749587 1.0000 120 chr3L:20990370-20990490 1.0000 120 chr3R:30843212-30843332 1.0000 120 chr3L:10757099-10757219 1.0000 120 chr2L:21006713-21006833 1.0000 120 chr2L:15392514-15392634 1.0000 120 chr2R:21799528-21799648 1.0000 120 chr3L:6364407-6364527 1.0000 120 chr3R:20283373-20283493 1.0000 120 chr3L:21594508-21594628 1.0000 120 chr3R:6954615-6954735 1.0000 120 chr2R:15745323-15745443 1.0000 120 chr2L:20956987-20957107 1.0000 120 chrX:8212237-8212357 1.0000 120 chr3R:26832024-26832144 1.0000 120 chrX:13936333-13936453 1.0000 120 chr3L:14610661-14610781 1.0000 120 chr3R:21648638-21648758 1.0000 120 chr2L:14995178-14995298 1.0000 120 chr2L:19200357-19200477 1.0000 120 chr3R:23878350-23878470 1.0000 120 chrX:18272570-18272690 1.0000 120 chr2L:16591520-16591640 1.0000 120 chrX:17518434-17518554 1.0000 120 chr2R:14317091-14317211 1.0000 120 chr3L:5851712-5851832 1.0000 120 chr2R:17831980-17832100 1.0000 120 chr2R:24807797-24807917 1.0000 120 chr2R:17499294-17499414 1.0000 120 chr3R:15596039-15596159 1.0000 120 chr3R:10455052-10455172 1.0000 120 chr3R:21948782-21948902 1.0000 120 chr3R:15556670-15556790 1.0000 120 chr3L:16489893-16490013 1.0000 120 chr3L:8881863-8881983 1.0000 120 chr3L:4731892-4732012 1.0000 120 chr2R:18926572-18926692 1.0000 120 chr2R:13438392-13438512 1.0000 120 chr2R:14929621-14929741 1.0000 120 chrX:17807137-17807257 1.0000 120 chr3L:3442196-3442316 1.0000 120 chr3L:13107469-13107589 1.0000 120 chr3R:9966195-9966315 1.0000 120 chr2L:609635-609755 1.0000 120 chrX:2336599-2336719 1.0000 120 chrX:17760709-17760829 1.0000 120 chr2L:608260-608380 1.0000 120 chr3R:7651134-7651254 1.0000 120 chr2R:22399531-22399651 1.0000 120 chr3R:19255433-19255553 1.0000 120 chr2R:12535193-12535313 1.0000 120 chr2L:16503019-16503139 1.0000 120 chrX:12507705-12507825 1.0000 120 chr3L:12915611-12915731 1.0000 120 chrX:7535000-7535120 1.0000 120 chr2R:15100678-15100798 1.0000 120 chrX:2455459-2455579 1.0000 120 chr2R:11183177-11183297 1.0000 120 chr3L:1320649-1320769 1.0000 120 chrX:10581670-10581790 1.0000 120 chr3L:14463951-14464071 1.0000 120 chr2L:13146453-13146573 1.0000 120 chr3L:2830155-2830275 1.0000 120 chr2L:7899314-7899434 1.0000 120 chr3R:31482261-31482381 1.0000 120 chr2R:16836450-16836570 1.0000 120 chrX:9068954-9069074 1.0000 120 chrX:21592140-21592260 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_fd59A/ -dna -nmotifs 5 -w 8 -maxsize 250000 -nostatus ../result/final_prediction/fly/fasta/RankLinear8.0_60/fd59A.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 0.162 G 0.156 T 0.337 Background letter frequencies (from file dataset with add-one prior applied): A 0.344 C 0.162 G 0.156 T 0.337 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF GCCCCMCG MEME-1 width = 8 sites = 10 llr = 107 E-value = 3.5e+003 ******************************************************************************** -------------------------------------------------------------------------------- Motif GCCCCMCG MEME-1 Description -------------------------------------------------------------------------------- Simplified A :::::6:3 pos.-specific C :a9a948: probability G 7:1:1:27 matrix T 3::::::: bits 2.7 * * 2.4 * * 2.1 **** 1.9 **** * Relative 1.6 **** * Entropy 1.3 ***** ** (15.4 bits) 1.1 ******** 0.8 ******** 0.5 ******** 0.3 ******** 0.0 -------- Multilevel GCCCCACG consensus T CGA sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCCCCMCG MEME-1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr2L:3562503-3562623 32 1.37e-06 TATGTACTTG GCCCCACG TTGGGCGCTA chrX:9068954-9069074 27 3.72e-06 CTTTGATAAT TCCCCCCG ATGTGCAGTG chr2L:15392514-15392634 113 3.72e-06 TATTCAAAAA TCCCCCCG chr3R:8107064-8107184 63 3.72e-06 TTCACACCAC TCCCCCCG TTTCCCACAC chr2L:7911471-7911591 68 4.62e-06 TTTTTATGAT GCCCCAGG GCCAATAGAA chr2L:1456999-1457119 79 8.69e-06 TTTTCTCAGT GCCCCACA CCCATAGACC chr3R:30259743-30259863 99 8.69e-06 AGAACAGAGA GCCCCACA TAATTACCCG chr2R:18567346-18567466 33 1.13e-05 GAGCTGGACA GCCCGACG TCCAGACAGT chr2R:11083884-11084004 40 1.13e-05 CTTGCTAAAG GCGCCACG TAAAACTTTG chr3L:14350986-14351106 91 1.32e-05 CGAACACAGA GCCCCCGA ATCCCGATGC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCCCCMCG MEME-1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr2L:3562503-3562623 1.4e-06 31_[+1]_81 chrX:9068954-9069074 3.7e-06 26_[+1]_86 chr2L:15392514-15392634 3.7e-06 112_[+1] chr3R:8107064-8107184 3.7e-06 62_[+1]_50 chr2L:7911471-7911591 4.6e-06 67_[+1]_45 chr2L:1456999-1457119 8.7e-06 78_[+1]_34 chr3R:30259743-30259863 8.7e-06 98_[+1]_14 chr2R:18567346-18567466 1.1e-05 32_[+1]_80 chr2R:11083884-11084004 1.1e-05 39_[+1]_73 chr3L:14350986-14351106 1.3e-05 90_[+1]_22 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCCCCMCG MEME-1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF GCCCCMCG width=8 seqs=10 chr2L:3562503-3562623 ( 32) GCCCCACG 1 chrX:9068954-9069074 ( 27) TCCCCCCG 1 chr2L:15392514-15392634 ( 113) TCCCCCCG 1 chr3R:8107064-8107184 ( 63) TCCCCCCG 1 chr2L:7911471-7911591 ( 68) GCCCCAGG 1 chr2L:1456999-1457119 ( 79) GCCCCACA 1 chr3R:30259743-30259863 ( 99) GCCCCACA 1 chr2R:18567346-18567466 ( 33) GCCCGACG 1 chr2R:11083884-11084004 ( 40) GCGCCACG 1 chr3L:14350986-14351106 ( 91) GCCCCCGA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCCCCMCG MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 28250 bayes= 11.7151 E= 3.5e+003 -997 -997 216 -17 -997 262 -997 -997 -997 247 -64 -997 -997 262 -997 -997 -997 247 -64 -997 80 130 -997 -997 -997 230 36 -997 -20 -997 216 -997 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCCCCMCG MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 10 E= 3.5e+003 0.000000 0.000000 0.700000 0.300000 0.000000 1.000000 0.000000 0.000000 0.000000 0.900000 0.100000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.900000 0.100000 0.000000 0.600000 0.400000 0.000000 0.000000 0.000000 0.800000 0.200000 0.000000 0.300000 0.000000 0.700000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCCCCMCG MEME-1 regular expression -------------------------------------------------------------------------------- [GT]CCCC[AC][CG][GA] -------------------------------------------------------------------------------- Time 7.49 secs. ******************************************************************************** ******************************************************************************** MOTIF CTGMGGGM MEME-2 width = 8 sites = 6 llr = 71 E-value = 7.7e+003 ******************************************************************************** -------------------------------------------------------------------------------- Motif CTGMGGGM MEME-2 Description -------------------------------------------------------------------------------- Simplified A :::3:::3 pos.-specific C a::7:::7 probability G :3a:aaa: matrix T :7:::::: bits 2.7 * * *** 2.4 * * *** 2.1 * * *** 1.9 * * *** Relative 1.6 * * *** Entropy 1.3 * ****** (17.0 bits) 1.1 ******** 0.8 ******** 0.5 ******** 0.3 ******** 0.0 -------- Multilevel CTGCGGGC consensus G A A sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTGMGGGM MEME-2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr2R:22399531-22399651 47 3.93e-07 ACTCATTCAG CGGCGGGC GATTCGCCAG chr2L:3154938-3155058 6 1.24e-06 TTATA CTGCGGGC CTCAACATAA chr2L:2484263-2484383 3 2.91e-06 AA CGGAGGGC AACACATGAT chr2R:11749467-11749587 78 6.51e-06 AATGCGTACA CTGCGGGA AATGTTCATT chr3R:29847243-29847363 3 6.51e-06 CA CTGCGGGA AATAGGGTTC chr2R:6515157-6515277 49 6.51e-06 AAGGAGACTT CTGAGGGC AGCAGATCCA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTGMGGGM MEME-2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr2R:22399531-22399651 3.9e-07 46_[+2]_66 chr2L:3154938-3155058 1.2e-06 5_[+2]_107 chr2L:2484263-2484383 2.9e-06 2_[+2]_110 chr2R:11749467-11749587 6.5e-06 77_[+2]_35 chr3R:29847243-29847363 6.5e-06 2_[+2]_110 chr2R:6515157-6515277 6.5e-06 48_[+2]_64 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTGMGGGM MEME-2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF CTGMGGGM width=8 seqs=6 chr2R:22399531-22399651 ( 47) CGGCGGGC 1 chr2L:3154938-3155058 ( 6) CTGCGGGC 1 chr2L:2484263-2484383 ( 3) CGGAGGGC 1 chr2R:11749467-11749587 ( 78) CTGCGGGA 1 chr3R:29847243-29847363 ( 3) CTGCGGGA 1 chr2R:6515157-6515277 ( 49) CTGAGGGC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTGMGGGM MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 28250 bayes= 13.3004 E= 7.7e+003 -923 262 -923 -923 -923 -923 109 98 -923 -923 268 -923 -5 204 -923 -923 -923 -923 268 -923 -923 -923 268 -923 -923 -923 268 -923 -5 204 -923 -923 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTGMGGGM MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 6 E= 7.7e+003 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.333333 0.666667 0.000000 0.000000 1.000000 0.000000 0.333333 0.666667 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.333333 0.666667 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTGMGGGM MEME-2 regular expression -------------------------------------------------------------------------------- C[TG]G[CA]GGG[CA] -------------------------------------------------------------------------------- Time 13.79 secs. ******************************************************************************** ******************************************************************************** MOTIF GCGCAGCC MEME-3 width = 8 sites = 2 llr = 28 E-value = 1.9e+004 ******************************************************************************** -------------------------------------------------------------------------------- Motif GCGCAGCC MEME-3 Description -------------------------------------------------------------------------------- Simplified A ::::a::: pos.-specific C :a:a::aa probability G a:a::a:: matrix T :::::::: bits 2.7 **** *** 2.4 **** *** 2.1 **** *** 1.9 **** *** Relative 1.6 ******** Entropy 1.3 ******** (20.1 bits) 1.1 ******** 0.8 ******** 0.5 ******** 0.3 ******** 0.0 -------- Multilevel GCGCAGCC consensus sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCGCAGCC MEME-3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr2L:5479238-5479358 26 8.99e-07 ATTTCCACAC GCGCAGCC AGGAGATGCA chrX:6778240-6778360 113 8.99e-07 CTCTAGACTG GCGCAGCC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCGCAGCC MEME-3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr2L:5479238-5479358 9e-07 25_[+3]_87 chrX:6778240-6778360 9e-07 112_[+3] -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCGCAGCC MEME-3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF GCGCAGCC width=8 seqs=2 chr2L:5479238-5479358 ( 26) GCGCAGCC 1 chrX:6778240-6778360 ( 113) GCGCAGCC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCGCAGCC MEME-3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 28250 bayes= 13.7859 E= 1.9e+004 -765 -765 267 -765 -765 262 -765 -765 -765 -765 267 -765 -765 262 -765 -765 153 -765 -765 -765 -765 -765 267 -765 -765 262 -765 -765 -765 262 -765 -765 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCGCAGCC MEME-3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 2 E= 1.9e+004 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 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 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCGCAGCC MEME-3 regular expression -------------------------------------------------------------------------------- GCGCAGCC -------------------------------------------------------------------------------- Time 20.08 secs. ******************************************************************************** ******************************************************************************** MOTIF GGAGCTGG MEME-4 width = 8 sites = 2 llr = 27 E-value = 2.1e+004 ******************************************************************************** -------------------------------------------------------------------------------- Motif GGAGCTGG MEME-4 Description -------------------------------------------------------------------------------- Simplified A ::a::::: pos.-specific C ::::a::: probability G aa:a::aa matrix T :::::a:: bits 2.7 ** ** ** 2.4 ** ** ** 2.1 ** ** ** 1.9 ** ** ** Relative 1.6 ******** Entropy 1.3 ******** (19.1 bits) 1.1 ******** 0.8 ******** 0.5 ******** 0.3 ******** 0.0 -------- Multilevel GGAGCTGG consensus sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGAGCTGG MEME-4 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr3L:21594508-21594628 18 1.74e-06 AACCTCGGTC GGAGCTGG GGCACACTGA chr2R:18567346-18567466 22 1.74e-06 ACTCTAGATA GGAGCTGG ACAGCCCGAC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGAGCTGG MEME-4 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr3L:21594508-21594628 1.7e-06 17_[+4]_95 chr2R:18567346-18567466 1.7e-06 21_[+4]_91 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGAGCTGG MEME-4 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF GGAGCTGG width=8 seqs=2 chr3L:21594508-21594628 ( 18) GGAGCTGG 1 chr2R:18567346-18567466 ( 22) GGAGCTGG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGAGCTGG MEME-4 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 28250 bayes= 13.7859 E= 2.1e+004 -765 -765 267 -765 -765 -765 267 -765 153 -765 -765 -765 -765 -765 267 -765 -765 262 -765 -765 -765 -765 -765 156 -765 -765 267 -765 -765 -765 267 -765 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGAGCTGG MEME-4 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 2 E= 2.1e+004 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGAGCTGG MEME-4 regular expression -------------------------------------------------------------------------------- GGAGCTGG -------------------------------------------------------------------------------- Time 26.35 secs. ******************************************************************************** ******************************************************************************** MOTIF TTGGGCGC MEME-5 width = 8 sites = 2 llr = 26 E-value = 2.6e+004 ******************************************************************************** -------------------------------------------------------------------------------- Motif TTGGGCGC MEME-5 Description -------------------------------------------------------------------------------- Simplified A :::::::: pos.-specific C :::::a:a probability G ::aaa:a: matrix T aa:::::: bits 2.7 ****** 2.4 ****** 2.1 ****** 1.9 ****** Relative 1.6 ******** Entropy 1.3 ******** (19.1 bits) 1.1 ******** 0.8 ******** 0.5 ******** 0.3 ******** 0.0 -------- Multilevel TTGGGCGC consensus sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTGGGCGC MEME-5 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr2L:608260-608380 109 1.77e-06 TGTTTTTACG TTGGGCGC CATA chr2L:3562503-3562623 40 1.77e-06 TGGCCCCACG TTGGGCGC TAGTTTCTGT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTGGGCGC MEME-5 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr2L:608260-608380 1.8e-06 108_[+5]_4 chr2L:3562503-3562623 1.8e-06 39_[+5]_73 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTGGGCGC MEME-5 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF TTGGGCGC width=8 seqs=2 chr2L:608260-608380 ( 109) TTGGGCGC 1 chr2L:3562503-3562623 ( 40) TTGGGCGC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTGGGCGC MEME-5 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 28250 bayes= 13.7859 E= 2.6e+004 -765 -765 -765 156 -765 -765 -765 156 -765 -765 267 -765 -765 -765 267 -765 -765 -765 267 -765 -765 262 -765 -765 -765 -765 267 -765 -765 262 -765 -765 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTGGGCGC MEME-5 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 2 E= 2.6e+004 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 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 1.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTGGGCGC MEME-5 regular expression -------------------------------------------------------------------------------- TTGGGCGC -------------------------------------------------------------------------------- Time 32.64 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrX:17355904-17356024 9.79e-01 120 chr2R:8318257-8318377 2.95e-01 120 chr2L:612846-612966 3.63e-01 120 chr2L:1574174-1574294 7.29e-01 120 chr2L:11966164-11966284 8.89e-01 120 chr2R:15483166-15483286 9.91e-01 120 chr3L:18245959-18246079 9.26e-01 120 chr3L:13288345-13288465 8.11e-01 120 chr2L:20940899-20941019 9.99e-01 120 chr2L:18946339-18946459 2.75e-01 120 chr3R:13851081-13851201 9.39e-01 120 chr2R:11551109-11551229 1.32e-01 120 chr3L:12455201-12455321 9.54e-01 120 chr2R:8995143-8995263 7.19e-01 120 chr2L:14569418-14569538 9.99e-01 120 chr3R:7025313-7025433 1.90e-01 95_[+3(9.89e-05)]_17 chr3R:8107064-8107184 3.28e-02 62_[+1(3.72e-06)]_50 chr2R:7848711-7848831 8.93e-01 120 chr3R:28999145-28999265 1.00e+00 120 chr3L:13178305-13178425 2.05e-01 120 chr3L:20988037-20988157 4.63e-01 120 chr2L:5288351-5288471 5.77e-01 120 chr2R:9498769-9498889 5.92e-01 120 chr3R:27175904-27176024 8.49e-02 20_[+1(1.53e-05)]_92 chr3L:14464671-14464791 9.38e-01 120 chr2L:19156629-19156749 5.70e-01 120 chr2R:8595873-8595993 1.98e-01 120 chr2L:3351978-3352098 1.29e-02 54_[+3(3.58e-05)]_58 chrX:9787540-9787660 4.74e-01 120 chr3L:16209173-16209293 7.20e-01 120 chr2R:15047009-15047129 3.40e-01 120 chr3L:8813626-8813746 9.92e-02 120 chrX:17351682-17351802 5.15e-02 120 chr2R:6515157-6515277 5.40e-04 48_[+2(6.51e-06)]_64 chr2L:3154938-3155058 6.14e-03 5_[+2(1.24e-06)]_107 chr3L:3338210-3338330 8.81e-01 120 chr2L:15388397-15388517 1.00e+00 120 chrX:18537527-18537647 3.99e-01 120 chr3L:17577048-17577168 5.21e-01 120 chr3R:30101055-30101175 6.29e-01 120 chr3R:24496221-24496341 9.92e-01 120 chr2L:7911471-7911591 9.15e-03 67_[+1(4.62e-06)]_45 chr3L:13066312-13066432 9.98e-01 120 chr2R:15000507-15000627 7.35e-01 120 chr2L:20936595-20936715 9.73e-01 120 chr3R:10177030-10177150 4.76e-01 120 chrX:6704079-6704199 5.96e-01 120 chr3L:8822394-8822514 2.22e-01 120 chr3L:3109487-3109607 9.99e-01 120 chr3R:10829938-10830058 6.70e-01 120 chr3R:6102517-6102637 4.45e-01 120 chrX:2880826-2880946 4.64e-01 120 chr2R:20578614-20578734 6.34e-01 120 chr2L:14572185-14572305 9.69e-01 120 chr3R:21653043-21653163 4.13e-01 120 chr2L:1312441-1312561 7.38e-01 120 chr2L:12840525-12840645 3.30e-02 39_[+1(9.53e-05)]_73 chr3L:14063556-14063676 5.32e-02 42_[+3(3.58e-05)]_70 chr3L:16484870-16484990 3.85e-01 120 chr3L:485054-485174 9.82e-01 120 chr3L:15220535-15220655 7.99e-01 120 chr2R:11083884-11084004 4.07e-04 39_[+1(1.13e-05)]_47_[+2(5.42e-05)]_\ 18 chrX:8800493-8800613 9.66e-01 120 chr3L:16941454-16941574 5.35e-01 120 chr2L:2485421-2485541 9.88e-01 120 chr3R:29091755-29091875 3.57e-01 120 chr2L:3562503-3562623 4.88e-07 31_[+1(1.37e-06)]_[+5(1.77e-06)]_73 chr3R:29011229-29011349 5.56e-01 120 chr2L:9736181-9736301 8.01e-01 120 chr3R:24953291-24953411 9.30e-01 120 chr2L:2484263-2484383 1.32e-03 2_[+2(2.91e-06)]_110 chrX:19843015-19843135 4.74e-01 120 chr2L:1455636-1455756 9.97e-01 120 chrX:379702-379822 9.93e-01 120 chr3R:21940271-21940391 9.51e-01 120 chr3R:30259743-30259863 3.94e-02 98_[+1(8.69e-06)]_14 chr3R:13846012-13846132 7.65e-01 120 chr3R:19070633-19070753 7.45e-01 120 chrX:14134093-14134213 9.93e-01 120 chr2R:22119894-22120014 4.43e-01 120 chr3R:24970764-24970884 5.90e-01 120 chr2L:5372652-5372772 9.76e-01 120 chr3L:18406043-18406163 9.94e-01 120 chr2L:20989586-20989706 7.21e-01 120 chr3L:1711364-1711484 3.02e-01 120 chr3L:14350986-14351106 1.43e-02 90_[+1(1.32e-05)]_22 chr3L:21721027-21721147 2.80e-01 120 chr2L:14665105-14665225 2.17e-01 120 chr3R:30264988-30265108 8.70e-01 120 chr2L:2073052-2073172 7.73e-01 120 chr2L:11399665-11399785 8.39e-01 120 chr3L:6355190-6355310 4.96e-01 120 chr3L:21043977-21044097 1.08e-01 120 chr2L:14529392-14529512 8.12e-01 120 chr2L:11069683-11069803 9.56e-01 120 chr2L:646654-646774 1.00e+00 120 chr3R:6106826-6106946 8.27e-01 120 chrX:17112110-17112230 6.52e-01 120 chr3R:13916689-13916809 9.73e-01 120 chr2L:3557595-3557715 9.09e-02 120 chr3L:20592702-20592822 2.94e-01 120 chr2R:21300866-21300986 8.71e-01 120 chrX:5301036-5301156 1.92e-01 120 chr3R:21826297-21826417 9.74e-01 120 chr3L:8284854-8284974 3.06e-01 120 chrX:7222251-7222371 8.27e-01 120 chrX:6778240-6778360 3.20e-04 112_[+3(8.99e-07)] chr3L:18078841-18078961 8.33e-01 120 chr3R:29847243-29847363 1.72e-02 2_[+2(6.51e-06)]_110 chr2R:18746909-18747029 3.23e-01 120 chrX:2358341-2358461 3.71e-01 120 chr2R:8749912-8750032 2.21e-01 12_[+3(3.58e-05)]_100 chr3L:16259751-16259871 1.92e-01 120 chrX:8747802-8747922 9.99e-01 120 chr3R:5053072-5053192 4.88e-01 120 chr3L:3106279-3106399 3.73e-01 120 chrX:4442675-4442795 1.63e-01 120 chr3R:16210873-16210993 8.24e-01 120 chr3R:30256364-30256484 9.77e-01 120 chr2L:3719614-3719734 1.43e-01 120 chr2R:11048106-11048226 6.75e-01 120 chr3L:15005910-15006030 5.45e-01 120 chr2R:21495518-21495638 6.91e-01 120 chr2R:18271189-18271309 6.61e-01 120 chr3R:14717353-14717473 9.16e-01 120 chr2R:19964416-19964536 9.11e-01 120 chr3L:10562399-10562519 8.70e-01 120 chr3L:4747518-4747638 6.93e-01 120 chrX:20482942-20483062 9.95e-01 120 chr3R:31319923-31320043 8.68e-01 120 chr3L:20582530-20582650 6.69e-01 120 chr3L:10913297-10913417 8.74e-02 120 chr3L:11382764-11382884 8.83e-01 120 chrX:14017549-14017669 9.81e-01 120 chr2R:21706440-21706560 5.86e-01 120 chr3R:8958435-8958555 9.76e-01 120 chrX:12511422-12511542 8.58e-01 120 chr3R:27222091-27222211 8.90e-01 120 chrX:9468445-9468565 2.38e-01 120 chr2L:5494021-5494141 9.00e-01 120 chr2R:21224995-21225115 2.30e-01 120 chr3R:10533296-10533416 8.57e-01 120 chr3L:10387674-10387794 4.01e-02 120 chr3R:9346661-9346781 9.10e-01 120 chr3R:5042552-5042672 9.70e-01 120 chr2R:23014898-23015018 7.26e-01 120 chr3L:3073678-3073798 4.77e-01 120 chr2L:1409831-1409951 7.19e-01 120 chr2R:13461339-13461459 6.57e-01 120 chr2L:11074082-11074202 9.62e-01 120 chr2L:11386494-11386614 2.10e-02 85_[+4(6.43e-05)]_27 chr3L:19961924-19962044 6.92e-01 120 chr2L:21847459-21847579 8.51e-01 120 chr2L:3582803-3582923 9.64e-01 120 chr3L:10968817-10968937 1.07e-01 120 chr2R:11033725-11033845 6.20e-01 120 chr3R:27199541-27199661 1.99e-01 120 chr2R:21847831-21847951 8.80e-01 120 chr2L:15909387-15909507 7.87e-01 120 chr2R:11544153-11544273 9.87e-01 120 chr3R:14389435-14389555 8.72e-01 120 chrX:5020191-5020311 9.99e-01 120 chr2L:8919786-8919906 3.02e-01 120 chr2R:7912153-7912273 8.95e-01 120 chr2L:19454518-19454638 9.22e-01 120 chr3R:18998457-18998577 4.97e-01 120 chr3L:8013453-8013573 3.91e-01 120 chr2L:1456999-1457119 5.08e-02 78_[+1(8.69e-06)]_34 chr3R:27179112-27179232 8.20e-01 120 chr2R:18567346-18567466 6.42e-06 21_[+4(1.74e-06)]_3_[+1(1.13e-05)]_\ 63_[+3(9.89e-05)]_9 chr3R:22184230-22184350 9.95e-01 120 chr3L:22743081-22743201 8.91e-01 120 chr3R:18485369-18485489 7.43e-02 120 chr2L:18517131-18517251 3.74e-01 120 chrX:8215614-8215734 9.42e-01 120 chr3L:21042714-21042834 7.97e-01 120 chrX:18929537-18929657 3.84e-01 120 chrX:18540311-18540431 2.55e-01 120 chr2L:4069653-4069773 1.00e+00 120 chr2L:4071679-4071799 6.41e-01 120 chr2L:5479238-5479358 3.95e-04 25_[+3(8.99e-07)]_87 chr3R:24143955-24144075 7.27e-01 120 chr2R:11749467-11749587 2.73e-02 77_[+2(6.51e-06)]_35 chr3L:20990370-20990490 9.99e-01 120 chr3R:30843212-30843332 7.95e-01 120 chr3L:10757099-10757219 9.04e-01 120 chr2L:21006713-21006833 1.82e-01 120 chr2L:15392514-15392634 2.01e-02 112_[+1(3.72e-06)] chr2R:21799528-21799648 4.10e-01 120 chr3L:6364407-6364527 4.88e-01 120 chr3R:20283373-20283493 6.75e-01 120 chr3L:21594508-21594628 1.68e-04 17_[+4(1.74e-06)]_95 chr3R:6954615-6954735 1.00e+00 120 chr2R:15745323-15745443 2.40e-01 120 chr2L:20956987-20957107 9.84e-01 120 chrX:8212237-8212357 9.89e-01 120 chr3R:26832024-26832144 2.70e-01 120 chrX:13936333-13936453 1.60e-01 120 chr3L:14610661-14610781 9.84e-01 120 chr3R:21648638-21648758 9.97e-01 120 chr2L:14995178-14995298 9.61e-01 120 chr2L:19200357-19200477 1.98e-01 120 chr3R:23878350-23878470 8.63e-01 120 chrX:18272570-18272690 8.28e-01 120 chr2L:16591520-16591640 2.41e-01 120 chrX:17518434-17518554 6.56e-01 120 chr2R:14317091-14317211 8.64e-01 120 chr3L:5851712-5851832 5.33e-01 120 chr2R:17831980-17832100 9.83e-01 120 chr2R:24807797-24807917 1.27e-01 120 chr2R:17499294-17499414 7.59e-01 120 chr3R:15596039-15596159 9.91e-01 120 chr3R:10455052-10455172 9.44e-01 120 chr3R:21948782-21948902 8.37e-02 120 chr3R:15556670-15556790 8.86e-01 120 chr3L:16489893-16490013 9.62e-01 120 chr3L:8881863-8881983 1.05e-01 120 chr3L:4731892-4732012 8.53e-01 120 chr2R:18926572-18926692 9.27e-01 120 chr2R:13438392-13438512 7.89e-01 120 chr2R:14929621-14929741 8.96e-01 120 chrX:17807137-17807257 9.48e-01 120 chr3L:3442196-3442316 8.64e-01 120 chr3L:13107469-13107589 4.59e-01 120 chr3R:9966195-9966315 8.57e-02 120 chr2L:609635-609755 2.17e-01 120 chrX:2336599-2336719 6.32e-01 120 chrX:17760709-17760829 9.98e-01 120 chr2L:608260-608380 9.30e-04 108_[+5(1.77e-06)]_4 chr3R:7651134-7651254 8.61e-01 120 chr2R:22399531-22399651 9.55e-05 46_[+2(3.93e-07)]_66 chr3R:19255433-19255553 8.78e-01 120 chr2R:12535193-12535313 9.90e-01 120 chr2L:16503019-16503139 2.64e-01 120 chrX:12507705-12507825 5.38e-01 120 chr3L:12915611-12915731 5.54e-01 120 chrX:7535000-7535120 6.26e-01 120 chr2R:15100678-15100798 7.43e-02 120 chrX:2455459-2455579 6.41e-01 120 chr2R:11183177-11183297 9.99e-01 120 chr3L:1320649-1320769 5.63e-01 120 chrX:10581670-10581790 5.19e-01 120 chr3L:14463951-14464071 9.28e-01 120 chr2L:13146453-13146573 8.16e-01 120 chr3L:2830155-2830275 9.35e-01 120 chr2L:7899314-7899434 5.22e-01 120 chr3R:31482261-31482381 5.11e-01 120 chr2R:16836450-16836570 6.28e-01 120 chrX:9068954-9069074 2.28e-03 26_[+1(3.72e-06)]_86 chrX:21592140-21592260 3.79e-01 120 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (5) found. ******************************************************************************** CPU: c27n05.farnam.hpc.yale.internal ********************************************************************************