******************************************************************************** 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/dmrt99B.fasta CONTROL SEQUENCES= --none-- ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ chr2R:12229672-12229792 1.0000 120 chrX:8206012-8206132 1.0000 120 chr3L:7811055-7811175 1.0000 120 chr3L:4720640-4720760 1.0000 120 chr3R:22328804-22328924 1.0000 120 chr2R:18564381-18564501 1.0000 120 chrX:8835246-8835366 1.0000 120 chr3L:18766334-18766454 1.0000 120 chr3L:4534071-4534191 1.0000 120 chr3R:26409900-26410020 1.0000 120 chr3L:6807629-6807749 1.0000 120 chr2R:14042688-14042808 1.0000 120 chrX:11846497-11846617 1.0000 120 chr3L:7086783-7086903 1.0000 120 chrX:15121917-15122037 1.0000 120 chrX:696232-696352 1.0000 120 chrX:11841809-11841929 1.0000 120 chr2R:24897733-24897853 1.0000 120 chr3R:23735159-23735279 1.0000 120 chrX:18670214-18670334 1.0000 120 chrX:10536022-10536142 1.0000 120 chr2R:23739462-23739582 1.0000 120 chr2R:17080881-17081001 1.0000 120 chrX:10564260-10564380 1.0000 120 chrX:6542465-6542585 1.0000 120 chr2L:20951442-20951562 1.0000 120 chr3R:18804647-18804767 1.0000 120 chr3L:15494384-15494504 1.0000 120 chr3L:17113369-17113489 1.0000 120 chr3R:10154409-10154529 1.0000 120 chr3R:8964071-8964191 1.0000 120 chrX:16867761-16867881 1.0000 120 chr3R:26242630-26242750 1.0000 120 chr2R:16847096-16847216 1.0000 120 chrX:3745314-3745434 1.0000 120 chrX:7550838-7550958 1.0000 120 chr3L:10786071-10786191 1.0000 120 chr3R:29705908-29706028 1.0000 120 chr2R:19794371-19794491 1.0000 120 chr3L:16825303-16825423 1.0000 120 chrX:17762401-17762521 1.0000 120 chr3L:18795604-18795724 1.0000 120 chr2L:8732872-8732992 1.0000 120 chr3L:3455047-3455167 1.0000 120 chr3R:24206035-24206155 1.0000 120 chr2L:20539362-20539482 1.0000 120 chr3R:29651609-29651729 1.0000 120 chr3L:19251733-19251853 1.0000 120 chr2L:2528231-2528351 1.0000 120 chrX:3768367-3768487 1.0000 120 chr3R:11663607-11663727 1.0000 120 chr2R:12236882-12237002 1.0000 120 chr2L:17229598-17229718 1.0000 120 chrX:8539139-8539259 1.0000 120 chr3R:13553271-13553391 1.0000 120 chrX:11848751-11848871 1.0000 120 chr2L:1916585-1916705 1.0000 120 chrX:5989519-5989639 1.0000 120 chr2L:7851757-7851877 1.0000 120 chr2L:18658224-18658344 1.0000 120 chr2R:21134027-21134147 1.0000 120 chr2R:14021975-14022095 1.0000 120 chrX:5847648-5847768 1.0000 120 chrX:16768926-16769046 1.0000 120 chrX:14727714-14727834 1.0000 120 chr3R:15117879-15117999 1.0000 120 chr2L:19252535-19252655 1.0000 120 chr2L:3100929-3101049 1.0000 120 chr3R:13549661-13549781 1.0000 120 chr3L:15923511-15923631 1.0000 120 chr3R:28623719-28623839 1.0000 120 chr3L:1869018-1869138 1.0000 120 chrX:17482962-17483082 1.0000 120 chr3L:5280090-5280210 1.0000 120 chr3L:10391106-10391226 1.0000 120 chr2R:11803306-11803426 1.0000 120 chr3R:27070382-27070502 1.0000 120 chrX:2861095-2861215 1.0000 120 chr3R:13907819-13907939 1.0000 120 chr3R:22719696-22719816 1.0000 120 chr3L:7262629-7262749 1.0000 120 chrX:16414603-16414723 1.0000 120 chr3L:10756187-10756307 1.0000 120 chrX:10233285-10233405 1.0000 120 chr3R:29717660-29717780 1.0000 120 chr3L:16697223-16697343 1.0000 120 chr3L:19338440-19338560 1.0000 120 chr3L:19670633-19670753 1.0000 120 chrX:15532202-15532322 1.0000 120 chrX:9911868-9911988 1.0000 120 chr3L:19231307-19231427 1.0000 120 chr3L:10428869-10428989 1.0000 120 chrX:3096447-3096567 1.0000 120 chr3L:917343-917463 1.0000 120 chrX:10741139-10741259 1.0000 120 chr3L:756559-756679 1.0000 120 chr3L:16054260-16054380 1.0000 120 chr2L:19373948-19374068 1.0000 120 chr3L:17226441-17226561 1.0000 120 chr3L:11444245-11444365 1.0000 120 chr2R:14305285-14305405 1.0000 120 chr3L:9033656-9033776 1.0000 120 chr3R:10498710-10498830 1.0000 120 chr2L:8552593-8552713 1.0000 120 chr3L:10536453-10536573 1.0000 120 chr2R:10681416-10681536 1.0000 120 chr2L:3569956-3570076 1.0000 120 chr3L:16482293-16482413 1.0000 120 chr3L:20710595-20710715 1.0000 120 chr2L:2731450-2731570 1.0000 120 chrX:12073763-12073883 1.0000 120 chr2R:24893716-24893836 1.0000 120 chrX:10397701-10397821 1.0000 120 chr3R:21837182-21837302 1.0000 120 chr2R:15073110-15073230 1.0000 120 chrX:13208236-13208356 1.0000 120 chr3L:19216537-19216657 1.0000 120 chr2R:18771127-18771247 1.0000 120 chr3L:2532536-2532656 1.0000 120 chrX:5095733-5095853 1.0000 120 chr2L:16869096-16869216 1.0000 120 chrX:9350432-9350552 1.0000 120 chr3L:7634900-7635020 1.0000 120 chr2R:14915050-14915170 1.0000 120 chrX:3740471-3740591 1.0000 120 chr3R:15293691-15293811 1.0000 120 chr3R:7591327-7591447 1.0000 120 chr3R:29004986-29005106 1.0000 120 chrX:22488434-22488554 1.0000 120 chr2R:12547641-12547761 1.0000 120 chr3L:517379-517499 1.0000 120 chr2L:5610211-5610331 1.0000 120 chrX:10718028-10718148 1.0000 120 chr3R:30461753-30461873 1.0000 120 chr2R:21895035-21895155 1.0000 120 chr3R:6233208-6233328 1.0000 120 chr2L:14123761-14123881 1.0000 120 chr3L:6157717-6157837 1.0000 120 chr3R:17955884-17956004 1.0000 120 chr2R:9184532-9184652 1.0000 120 chr3R:29690561-29690681 1.0000 120 chr3R:28904289-28904409 1.0000 120 chr2L:4861654-4861774 1.0000 120 chr2L:7492045-7492165 1.0000 120 chr2R:23003248-23003368 1.0000 120 chrX:3455552-3455672 1.0000 120 chr2R:7879093-7879213 1.0000 120 chr2L:3435234-3435354 1.0000 120 chr2L:18548891-18549011 1.0000 120 chr3L:9695752-9695872 1.0000 120 chr3L:19074006-19074126 1.0000 120 chr2L:1646740-1646860 1.0000 120 chr3R:13892980-13893100 1.0000 120 chr2L:20808303-20808423 1.0000 120 chrX:3019754-3019874 1.0000 120 chr2R:15134282-15134402 1.0000 120 chrX:19106977-19107097 1.0000 120 chr3R:6241378-6241498 1.0000 120 chr3R:8920206-8920326 1.0000 120 chr2R:17206010-17206130 1.0000 120 chrX:7095010-7095130 1.0000 120 chr3L:2845309-2845429 1.0000 120 chr3L:764456-764576 1.0000 120 chrX:9119399-9119519 1.0000 120 chr2R:19860377-19860497 1.0000 120 chr2R:23202154-23202274 1.0000 120 chrX:12937942-12938062 1.0000 120 chrX:3714162-3714282 1.0000 120 chrX:335008-335128 1.0000 120 chr3R:26900089-26900209 1.0000 120 chrX:342547-342667 1.0000 120 chr3R:15425732-15425852 1.0000 120 chr3R:6353010-6353130 1.0000 120 chr2R:13996681-13996801 1.0000 120 chrX:16580084-16580204 1.0000 120 chr2L:7966158-7966278 1.0000 120 chr3R:26333421-26333541 1.0000 120 chr3L:3380573-3380693 1.0000 120 chr3L:6482979-6483099 1.0000 120 chr3R:14095551-14095671 1.0000 120 chr3L:7592247-7592367 1.0000 120 chr2L:9564634-9564754 1.0000 120 chr2R:18273490-18273610 1.0000 120 chr3L:21738559-21738679 1.0000 120 chr3R:6414876-6414996 1.0000 120 chr3R:12451541-12451661 1.0000 120 chrX:13226632-13226752 1.0000 120 chrX:6439626-6439746 1.0000 120 chr3L:14363265-14363385 1.0000 120 chrX:17782137-17782257 1.0000 120 chrX:966955-967075 1.0000 120 chr2R:22529777-22529897 1.0000 120 chr3R:12562143-12562263 1.0000 120 chr2R:14915250-14915370 1.0000 120 chr2L:7266106-7266226 1.0000 120 chrX:6067621-6067741 1.0000 120 chr3R:28959266-28959386 1.0000 120 chr2L:19930224-19930344 1.0000 120 chr3R:21612988-21613108 1.0000 120 chr3R:29089814-29089934 1.0000 120 chr2L:3851456-3851576 1.0000 120 chrX:17726691-17726811 1.0000 120 chr3L:10337768-10337888 1.0000 120 chr2L:1619267-1619387 1.0000 120 chr3L:21859760-21859880 1.0000 120 chr2R:12951525-12951645 1.0000 120 chr3R:29699354-29699474 1.0000 120 chr3L:13917949-13918069 1.0000 120 chr3R:21420057-21420177 1.0000 120 chr3L:4353774-4353894 1.0000 120 chr3R:22108445-22108565 1.0000 120 chr3R:19014946-19015066 1.0000 120 chr3R:29581637-29581757 1.0000 120 chr2R:20195231-20195351 1.0000 120 chr3L:775103-775223 1.0000 120 chr2L:7150956-7151076 1.0000 120 chr3L:11285278-11285398 1.0000 120 chr3L:11291642-11291762 1.0000 120 chr3L:10767316-10767436 1.0000 120 chr3R:8469848-8469968 1.0000 120 chr2R:18994155-18994275 1.0000 120 chr2L:13876795-13876915 1.0000 120 chr3R:23067524-23067644 1.0000 120 chr2R:10160317-10160437 1.0000 120 chr3R:16769538-16769658 1.0000 120 chr3L:3970524-3970644 1.0000 120 chrX:11379261-11379381 1.0000 120 chrX:14213627-14213747 1.0000 120 chr3L:18272442-18272562 1.0000 120 chr3L:18114112-18114232 1.0000 120 chrX:10573655-10573775 1.0000 120 chr2R:7054352-7054472 1.0000 120 chr2R:23578524-23578644 1.0000 120 chr2L:17558239-17558359 1.0000 120 chr3R:5413061-5413181 1.0000 120 chr3R:30164200-30164320 1.0000 120 chr2R:11178527-11178647 1.0000 120 chr3L:10893529-10893649 1.0000 120 chr3R:10648930-10649050 1.0000 120 chr3L:3786913-3787033 1.0000 120 chr3L:20276750-20276870 1.0000 120 chr3L:5952166-5952286 1.0000 120 chr3L:10745698-10745818 1.0000 120 chrX:13764550-13764670 1.0000 120 chr3R:14875709-14875829 1.0000 120 chr3R:9344927-9345047 1.0000 120 chr2L:9206530-9206650 1.0000 120 chr2R:8734645-8734765 1.0000 120 chr3R:10449136-10449256 1.0000 120 chr3L:11408890-11409010 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_dmrt99B/ -dna -nmotifs 5 -w 8 -maxsize 250000 -nostatus ../result/final_prediction/fly/fasta/RankLinear8.0_60/dmrt99B.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 0.366 C 0.137 G 0.133 T 0.364 Background letter frequencies (from file dataset with add-one prior applied): A 0.366 C 0.137 G 0.133 T 0.364 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF CTGCWGGG MEME-1 width = 8 sites = 3 llr = 40 E-value = 1.0e+004 ******************************************************************************** -------------------------------------------------------------------------------- Motif CTGCWGGG MEME-1 Description -------------------------------------------------------------------------------- Simplified A ::::3::: pos.-specific C a::a:::: probability G ::a::aaa matrix T :a::7::: bits 2.9 * ** *** 2.6 * ** *** 2.3 * ** *** 2.0 * ** *** Relative 1.7 * ** *** Entropy 1.5 **** *** (19.4 bits) 1.2 **** *** 0.9 **** *** 0.6 ******** 0.3 ******** 0.0 -------- Multilevel CTGCTGGG consensus A sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTGCWGGG MEME-1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr3R:26900089-26900209 20 7.78e-07 TAAGTGCGTG CTGCTGGG GAATGATGAT chr2R:10681416-10681536 39 7.78e-07 AGTTGACAAT CTGCTGGG ATTTTTCTAA chr2R:16847096-16847216 102 1.56e-06 GATACTGATA CTGCAGGG TATTGCTTAT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTGCWGGG MEME-1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr3R:26900089-26900209 7.8e-07 19_[+1]_93 chr2R:10681416-10681536 7.8e-07 38_[+1]_74 chr2R:16847096-16847216 1.6e-06 101_[+1]_11 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTGCWGGG MEME-1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF CTGCWGGG width=8 seqs=3 chr3R:26900089-26900209 ( 20) CTGCTGGG 1 chr2R:10681416-10681536 ( 39) CTGCTGGG 1 chr2R:16847096-16847216 ( 102) CTGCAGGG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTGCWGGG MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 28250 bayes= 12.8598 E= 1.0e+004 -823 287 -823 -823 -823 -823 -823 146 -823 -823 290 -823 -823 287 -823 -823 -14 -823 -823 87 -823 -823 290 -823 -823 -823 290 -823 -823 -823 290 -823 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTGCWGGG MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 3 E= 1.0e+004 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 1.000000 0.000000 0.000000 0.333333 0.000000 0.000000 0.666667 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTGCWGGG MEME-1 regular expression -------------------------------------------------------------------------------- CTGC[TA]GGG -------------------------------------------------------------------------------- Time 7.52 secs. ******************************************************************************** ******************************************************************************** MOTIF GYGAGCTG MEME-2 width = 8 sites = 7 llr = 79 E-value = 2.7e+004 ******************************************************************************** -------------------------------------------------------------------------------- Motif GYGAGCTG MEME-2 Description -------------------------------------------------------------------------------- Simplified A :137:::: pos.-specific C :4:3:a:: probability G a:7:a::a matrix T :4::::a: bits 2.9 * ** * 2.6 * ** * 2.3 * ** * 2.0 * ** * Relative 1.7 * * ** * Entropy 1.5 * * **** (16.3 bits) 1.2 * * **** 0.9 * ****** 0.6 ******** 0.3 ******** 0.0 -------- Multilevel GCGAGCTG consensus TAC sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GYGAGCTG MEME-2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr2R:11178527-11178647 37 1.08e-06 CCAAGATGAA GCGAGCTG AGGATACCCC chrX:17482962-17483082 17 1.85e-06 GCAAACATAT GTGCGCTG GAAAAGTGTG chr3R:8920206-8920326 71 3.93e-06 TAAATTTCTT GTGAGCTG CAGCCAAAAA chr2L:2731450-2731570 113 3.93e-06 CCCATTGTGA GTGAGCTG chrX:14213627-14213747 53 6.89e-06 CTTAAGATAG GCAAGCTG GTTTTTTTTA chr3L:3455047-3455167 46 6.89e-06 AGCATGCTTA GCAAGCTG CACTTAGTTC chr2L:1916585-1916705 18 7.67e-06 ACTGGCAGTT GAGCGCTG GATGGCATTT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GYGAGCTG MEME-2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr2R:11178527-11178647 1.1e-06 36_[+2]_76 chrX:17482962-17483082 1.9e-06 16_[+2]_96 chr3R:8920206-8920326 3.9e-06 70_[+2]_42 chr2L:2731450-2731570 3.9e-06 112_[+2] chrX:14213627-14213747 6.9e-06 52_[+2]_60 chr3L:3455047-3455167 6.9e-06 45_[+2]_67 chr2L:1916585-1916705 7.7e-06 17_[+2]_95 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GYGAGCTG MEME-2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF GYGAGCTG width=8 seqs=7 chr2R:11178527-11178647 ( 37) GCGAGCTG 1 chrX:17482962-17483082 ( 17) GTGCGCTG 1 chr3R:8920206-8920326 ( 71) GTGAGCTG 1 chr2L:2731450-2731570 ( 113) GTGAGCTG 1 chrX:14213627-14213747 ( 53) GCAAGCTG 1 chr3L:3455047-3455167 ( 46) GCAAGCTG 1 chr2L:1916585-1916705 ( 18) GAGCGCTG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GYGAGCTG MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 28250 bayes= 12.5841 E= 2.7e+004 -945 -945 291 -945 -136 165 -945 24 -36 -945 242 -945 96 106 -945 -945 -945 -945 291 -945 -945 287 -945 -945 -945 -945 -945 146 -945 -945 291 -945 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GYGAGCTG MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 7 E= 2.7e+004 0.000000 0.000000 1.000000 0.000000 0.142857 0.428571 0.000000 0.428571 0.285714 0.000000 0.714286 0.000000 0.714286 0.285714 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 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GYGAGCTG MEME-2 regular expression -------------------------------------------------------------------------------- G[CT][GA][AC]GCTG -------------------------------------------------------------------------------- Time 13.79 secs. ******************************************************************************** ******************************************************************************** MOTIF GCGGCGSG MEME-3 width = 8 sites = 5 llr = 59 E-value = 3.4e+004 ******************************************************************************** -------------------------------------------------------------------------------- Motif GCGGCGSG MEME-3 Description -------------------------------------------------------------------------------- Simplified A 222::::: pos.-specific C :8::a:4: probability G 8:88:86a matrix T :::2:2:: bits 2.9 * * 2.6 * * 2.3 * * 2.0 * ****** Relative 1.7 ******** Entropy 1.5 ******** (17.1 bits) 1.2 ******** 0.9 ******** 0.6 ******** 0.3 ******** 0.0 -------- Multilevel GCGGCGGG consensus AAAT TC sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCGGCGSG MEME-3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr3R:10648930-10649050 8 1.63e-06 TCAAAAA GAGGCGGG ATTTCAGTAG chr2R:14915050-14915170 18 1.63e-06 ATAAATCAAT GCAGCGGG CACACAGAGA chr3L:17226441-17226561 92 1.63e-06 atatttaAAA GCGGCTGG AAATGATGGC chr3R:6233208-6233328 27 3.09e-06 GCAGATTCTA GCGTCGCG GACGCAGAAT chr3L:756559-756679 106 3.09e-06 GGAAGCTTAA ACGGCGCG ACCATCT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCGGCGSG MEME-3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr3R:10648930-10649050 1.6e-06 7_[+3]_105 chr2R:14915050-14915170 1.6e-06 17_[+3]_95 chr3L:17226441-17226561 1.6e-06 91_[+3]_21 chr3R:6233208-6233328 3.1e-06 26_[+3]_86 chr3L:756559-756679 3.1e-06 105_[+3]_7 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCGGCGSG MEME-3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF GCGGCGSG width=8 seqs=5 chr3R:10648930-10649050 ( 8) GAGGCGGG 1 chr2R:14915050-14915170 ( 18) GCAGCGGG 1 chr3L:17226441-17226561 ( 92) GCGGCTGG 1 chr3R:6233208-6233328 ( 27) GCGTCGCG 1 chr3L:756559-756679 ( 106) ACGGCGCG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCGGCGSG MEME-3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 28250 bayes= 13.4073 E= 3.4e+004 -87 -897 258 -897 -87 255 -897 -897 -87 -897 258 -897 -897 -897 258 -86 -897 287 -897 -897 -897 -897 258 -86 -897 155 217 -897 -897 -897 291 -897 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCGGCGSG MEME-3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 5 E= 3.4e+004 0.200000 0.000000 0.800000 0.000000 0.200000 0.800000 0.000000 0.000000 0.200000 0.000000 0.800000 0.000000 0.000000 0.000000 0.800000 0.200000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.800000 0.200000 0.000000 0.400000 0.600000 0.000000 0.000000 0.000000 1.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCGGCGSG MEME-3 regular expression -------------------------------------------------------------------------------- [GA][CA][GA][GT]C[GT][GC]G -------------------------------------------------------------------------------- Time 20.08 secs. ******************************************************************************** ******************************************************************************** MOTIF GCASCKCC MEME-4 width = 8 sites = 3 llr = 39 E-value = 4.2e+004 ******************************************************************************** -------------------------------------------------------------------------------- Motif GCASCKCC MEME-4 Description -------------------------------------------------------------------------------- Simplified A ::7::::: pos.-specific C :a37a:aa probability G a::3:7:: matrix T :::::3:: bits 2.9 ** * ** 2.6 ** * ** 2.3 ** * ** 2.0 ** ** ** Relative 1.7 ** ** ** Entropy 1.5 ** ***** (18.9 bits) 1.2 ** ***** 0.9 ******** 0.6 ******** 0.3 ******** 0.0 -------- Multilevel GCACCGCC consensus CG T sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCASCKCC MEME-4 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chrX:10233285-10233405 30 4.29e-07 TACTTTACAA GCACCGCC CTTTTTTATT chrX:14213627-14213747 36 5.43e-07 CATTTCATGA GCCGCGCC TTAAGATAGG chr2R:22529777-22529897 91 2.02e-06 TTTTCCTTGT GCACCTCC TGCTTCACAA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCASCKCC MEME-4 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrX:10233285-10233405 4.3e-07 29_[+4]_83 chrX:14213627-14213747 5.4e-07 35_[+4]_77 chr2R:22529777-22529897 2e-06 90_[+4]_22 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCASCKCC MEME-4 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF GCASCKCC width=8 seqs=3 chrX:10233285-10233405 ( 30) GCACCGCC 1 chrX:14213627-14213747 ( 36) GCCGCGCC 1 chr2R:22529777-22529897 ( 91) GCACCTCC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCASCKCC MEME-4 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 28250 bayes= 12.8598 E= 4.2e+004 -823 -823 290 -823 -823 287 -823 -823 86 128 -823 -823 -823 228 132 -823 -823 287 -823 -823 -823 -823 232 -13 -823 287 -823 -823 -823 287 -823 -823 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCASCKCC MEME-4 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 3 E= 4.2e+004 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.666667 0.333333 0.000000 0.000000 0.000000 0.666667 0.333333 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.666667 0.333333 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCASCKCC MEME-4 regular expression -------------------------------------------------------------------------------- GC[AC][CG]C[GT]CC -------------------------------------------------------------------------------- Time 26.32 secs. ******************************************************************************** ******************************************************************************** MOTIF TGCTGSCC MEME-5 width = 8 sites = 2 llr = 27 E-value = 2.5e+004 ******************************************************************************** -------------------------------------------------------------------------------- Motif TGCTGSCC MEME-5 Description -------------------------------------------------------------------------------- Simplified A :::::::: pos.-specific C ::a::5aa probability G :a::a5:: matrix T a::a:::: bits 2.9 ** * ** 2.6 ** * ** 2.3 ** * ** 2.0 ** * ** Relative 1.7 ** **** Entropy 1.5 ******** (19.2 bits) 1.2 ******** 0.9 ******** 0.6 ******** 0.3 ******** 0.0 -------- Multilevel TGCTGCCC consensus G sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TGCTGSCC MEME-5 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr2R:23202154-23202274 1 8.02e-07 . TGCTGGCC AATCTGAGAT chr3L:756559-756679 47 1.63e-06 TGCTAGGATA TGCTGCCC CAGTGGTTTT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TGCTGSCC MEME-5 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr2R:23202154-23202274 8e-07 [+5]_112 chr3L:756559-756679 1.6e-06 46_[+5]_66 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TGCTGSCC MEME-5 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF TGCTGSCC width=8 seqs=2 chr2R:23202154-23202274 ( 1) TGCTGGCC 1 chr3L:756559-756679 ( 47) TGCTGCCC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TGCTGSCC MEME-5 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 28250 bayes= 12.9378 E= 2.5e+004 -765 -765 -765 145 -765 -765 290 -765 -765 286 -765 -765 -765 -765 -765 145 -765 -765 290 -765 -765 187 190 -765 -765 286 -765 -765 -765 286 -765 -765 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TGCTGSCC MEME-5 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 2 E= 2.5e+004 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 0.500000 0.500000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TGCTGSCC MEME-5 regular expression -------------------------------------------------------------------------------- TGCTG[CG]CC -------------------------------------------------------------------------------- Time 32.53 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr2R:12229672-12229792 5.30e-01 120 chrX:8206012-8206132 8.87e-01 120 chr3L:7811055-7811175 6.77e-01 120 chr3L:4720640-4720760 9.81e-01 120 chr3R:22328804-22328924 8.71e-01 120 chr2R:18564381-18564501 1.37e-01 44_[+5(8.40e-05)]_68 chrX:8835246-8835366 3.44e-01 120 chr3L:18766334-18766454 4.73e-01 120 chr3L:4534071-4534191 3.03e-01 120 chr3R:26409900-26410020 4.32e-01 120 chr3L:6807629-6807749 3.99e-01 120 chr2R:14042688-14042808 8.03e-01 120 chrX:11846497-11846617 5.38e-01 120 chr3L:7086783-7086903 1.23e-01 120 chrX:15121917-15122037 9.95e-01 120 chrX:696232-696352 9.25e-01 120 chrX:11841809-11841929 9.98e-01 120 chr2R:24897733-24897853 2.31e-01 120 chr3R:23735159-23735279 9.04e-04 15_[+1(6.52e-05)]_97 chrX:18670214-18670334 1.56e-01 120 chrX:10536022-10536142 6.82e-02 120 chr2R:23739462-23739582 7.22e-01 120 chr2R:17080881-17081001 2.79e-01 120 chrX:10564260-10564380 4.05e-01 120 chrX:6542465-6542585 1.00e+00 120 chr2L:20951442-20951562 2.79e-01 120 chr3R:18804647-18804767 9.79e-01 120 chr3L:15494384-15494504 1.52e-01 120 chr3L:17113369-17113489 2.04e-01 91_[+4(8.22e-05)]_21 chr3R:10154409-10154529 3.80e-01 120 chr3R:8964071-8964191 6.42e-01 120 chrX:16867761-16867881 8.86e-01 120 chr3R:26242630-26242750 2.60e-01 120 chr2R:16847096-16847216 3.18e-03 101_[+1(1.56e-06)]_11 chrX:3745314-3745434 9.06e-01 120 chrX:7550838-7550958 9.02e-01 120 chr3L:10786071-10786191 8.09e-02 63_[+1(3.50e-05)]_49 chr3R:29705908-29706028 4.52e-01 120 chr2R:19794371-19794491 8.08e-01 120 chr3L:16825303-16825423 1.21e-01 120 chrX:17762401-17762521 2.28e-01 120 chr3L:18795604-18795724 8.43e-01 120 chr2L:8732872-8732992 4.78e-02 120 chr3L:3455047-3455167 2.00e-03 45_[+2(6.89e-06)]_67 chr3R:24206035-24206155 6.92e-01 120 chr2L:20539362-20539482 3.66e-02 120 chr3R:29651609-29651729 5.70e-01 120 chr3L:19251733-19251853 9.89e-01 120 chr2L:2528231-2528351 2.97e-01 120 chrX:3768367-3768487 1.01e-02 120 chr3R:11663607-11663727 5.25e-01 120 chr2R:12236882-12237002 9.70e-01 120 chr2L:17229598-17229718 7.12e-01 120 chrX:8539139-8539259 7.32e-01 120 chr3R:13553271-13553391 6.02e-01 120 chrX:11848751-11848871 8.47e-01 120 chr2L:1916585-1916705 1.38e-03 17_[+2(7.67e-06)]_95 chrX:5989519-5989639 3.16e-01 120 chr2L:7851757-7851877 4.64e-01 120 chr2L:18658224-18658344 9.48e-01 120 chr2R:21134027-21134147 9.98e-01 120 chr2R:14021975-14022095 7.18e-01 120 chrX:5847648-5847768 3.34e-03 49_[+2(3.64e-05)]_63 chrX:16768926-16769046 5.42e-01 120 chrX:14727714-14727834 9.25e-02 120 chr3R:15117879-15117999 1.27e-03 98_[+5(6.37e-05)]_14 chr2L:19252535-19252655 8.60e-01 120 chr2L:3100929-3101049 1.11e-01 120 chr3R:13549661-13549781 9.59e-01 120 chr3L:15923511-15923631 9.32e-01 120 chr3R:28623719-28623839 5.78e-01 120 chr3L:1869018-1869138 5.14e-02 120 chrX:17482962-17483082 1.74e-04 16_[+2(1.85e-06)]_5_[+2(3.64e-05)]_\ 83 chr3L:5280090-5280210 9.93e-01 120 chr3L:10391106-10391226 9.44e-01 120 chr2R:11803306-11803426 8.28e-01 120 chr3R:27070382-27070502 5.62e-01 120 chrX:2861095-2861215 5.88e-01 120 chr3R:13907819-13907939 1.59e-01 120 chr3R:22719696-22719816 1.95e-01 120 chr3L:7262629-7262749 5.60e-01 120 chrX:16414603-16414723 4.41e-03 3_[+1(3.50e-05)]_109 chr3L:10756187-10756307 6.03e-01 120 chrX:10233285-10233405 8.84e-04 29_[+4(4.29e-07)]_83 chr3R:29717660-29717780 4.31e-01 120 chr3L:16697223-16697343 1.79e-01 120 chr3L:19338440-19338560 9.96e-01 120 chr3L:19670633-19670753 2.86e-01 120 chrX:15532202-15532322 6.03e-01 120 chrX:9911868-9911988 9.46e-01 120 chr3L:19231307-19231427 5.62e-01 120 chr3L:10428869-10428989 8.60e-01 120 chrX:3096447-3096567 5.01e-01 120 chr3L:917343-917463 9.33e-01 120 chrX:10741139-10741259 8.31e-01 120 chr3L:756559-756679 2.23e-08 35_[+1(3.50e-05)]_3_[+5(1.63e-06)]_\ 51_[+3(3.09e-06)]_7 chr3L:16054260-16054380 9.73e-01 120 chr2L:19373948-19374068 1.23e-01 120 chr3L:17226441-17226561 3.08e-04 91_[+3(1.63e-06)]_21 chr3L:11444245-11444365 9.99e-01 120 chr2R:14305285-14305405 5.08e-01 120 chr3L:9033656-9033776 9.01e-01 120 chr3R:10498710-10498830 4.61e-01 120 chr2L:8552593-8552713 5.41e-01 120 chr3L:10536453-10536573 5.92e-01 120 chr2R:10681416-10681536 1.78e-03 38_[+1(7.78e-07)]_74 chr2L:3569956-3570076 4.30e-01 120 chr3L:16482293-16482413 1.19e-01 120 chr3L:20710595-20710715 4.40e-01 120 chr2L:2731450-2731570 5.99e-04 112_[+2(3.93e-06)] chrX:12073763-12073883 8.87e-01 120 chr2R:24893716-24893836 4.31e-01 120 chrX:10397701-10397821 7.41e-02 120 chr3R:21837182-21837302 5.70e-01 120 chr2R:15073110-15073230 5.44e-01 120 chrX:13208236-13208356 1.00e+00 120 chr3L:19216537-19216657 6.64e-01 120 chr2R:18771127-18771247 3.11e-01 120 chr3L:2532536-2532656 7.08e-01 120 chrX:5095733-5095853 6.81e-01 120 chr2L:16869096-16869216 9.53e-01 120 chrX:9350432-9350552 1.00e+00 120 chr3L:7634900-7635020 9.01e-01 120 chr2R:14915050-14915170 1.74e-04 17_[+3(1.63e-06)]_95 chrX:3740471-3740591 3.53e-01 120 chr3R:15293691-15293811 7.67e-01 120 chr3R:7591327-7591447 1.37e-01 120 chr3R:29004986-29005106 2.58e-01 120 chrX:22488434-22488554 5.64e-02 120 chr2R:12547641-12547761 8.58e-01 120 chr3L:517379-517499 8.59e-01 120 chr2L:5610211-5610331 2.88e-03 120 chrX:10718028-10718148 2.89e-02 120 chr3R:30461753-30461873 8.28e-03 120 chr2R:21895035-21895155 6.27e-01 120 chr3R:6233208-6233328 5.44e-03 26_[+3(3.09e-06)]_86 chr2L:14123761-14123881 1.57e-02 120 chr3L:6157717-6157837 6.83e-01 120 chr3R:17955884-17956004 8.54e-01 120 chr2R:9184532-9184652 7.59e-01 120 chr3R:29690561-29690681 2.33e-01 120 chr3R:28904289-28904409 9.91e-01 120 chr2L:4861654-4861774 3.95e-01 120 chr2L:7492045-7492165 3.95e-02 120 chr2R:23003248-23003368 2.44e-02 120 chrX:3455552-3455672 9.76e-01 120 chr2R:7879093-7879213 9.68e-01 120 chr2L:3435234-3435354 1.42e-01 120 chr2L:18548891-18549011 9.97e-01 120 chr3L:9695752-9695872 4.56e-01 120 chr3L:19074006-19074126 9.99e-01 120 chr2L:1646740-1646860 4.10e-01 120 chr3R:13892980-13893100 6.64e-01 120 chr2L:20808303-20808423 7.24e-01 120 chrX:3019754-3019874 6.07e-01 120 chr2R:15134282-15134402 1.72e-01 120 chrX:19106977-19107097 5.36e-01 120 chr3R:6241378-6241498 3.62e-01 120 chr3R:8920206-8920326 6.88e-04 70_[+2(3.93e-06)]_42 chr2R:17206010-17206130 8.47e-01 120 chrX:7095010-7095130 4.80e-02 120 chr3L:2845309-2845429 2.88e-02 120 chr3L:764456-764576 5.18e-01 120 chrX:9119399-9119519 3.12e-03 120 chr2R:19860377-19860497 6.16e-01 120 chr2R:23202154-23202274 1.89e-04 [+5(8.02e-07)]_23_[+4(2.20e-05)]_81 chrX:12937942-12938062 9.95e-01 120 chrX:3714162-3714282 4.11e-01 120 chrX:335008-335128 8.35e-01 120 chr3R:26900089-26900209 1.72e-06 19_[+1(7.78e-07)]_93 chrX:342547-342667 1.19e-01 120 chr3R:15425732-15425852 3.82e-01 7_[+3(9.78e-05)]_105 chr3R:6353010-6353130 2.42e-01 120 chr2R:13996681-13996801 9.76e-01 120 chrX:16580084-16580204 7.64e-02 120 chr2L:7966158-7966278 8.37e-01 120 chr3R:26333421-26333541 6.81e-01 120 chr3L:3380573-3380693 4.06e-03 120 chr3L:6482979-6483099 2.41e-02 120 chr3R:14095551-14095671 7.24e-01 120 chr3L:7592247-7592367 3.86e-01 120 chr2L:9564634-9564754 3.00e-01 120 chr2R:18273490-18273610 6.20e-01 120 chr3L:21738559-21738679 6.13e-01 120 chr3R:6414876-6414996 1.00e+00 120 chr3R:12451541-12451661 8.25e-01 120 chrX:13226632-13226752 9.29e-01 120 chrX:6439626-6439746 6.44e-01 120 chr3L:14363265-14363385 1.62e-01 120 chrX:17782137-17782257 7.31e-01 120 chrX:966955-967075 2.44e-01 120 chr2R:22529777-22529897 8.87e-03 90_[+4(2.02e-06)]_22 chr3R:12562143-12562263 9.78e-01 120 chr2R:14915250-14915370 7.05e-01 120 chr2L:7266106-7266226 4.49e-02 93_[+5(6.37e-05)]_19 chrX:6067621-6067741 5.97e-01 120 chr3R:28959266-28959386 6.96e-01 120 chr2L:19930224-19930344 3.18e-01 120 chr3R:21612988-21613108 8.51e-01 120 chr3R:29089814-29089934 6.04e-01 120 chr2L:3851456-3851576 9.51e-01 120 chrX:17726691-17726811 9.19e-01 120 chr3L:10337768-10337888 9.43e-02 120 chr2L:1619267-1619387 8.16e-03 19_[+5(3.73e-05)]_93 chr3L:21859760-21859880 9.22e-01 120 chr2R:12951525-12951645 2.50e-01 120 chr3R:29699354-29699474 3.97e-01 120 chr3L:13917949-13918069 6.49e-01 120 chr3R:21420057-21420177 9.79e-02 120 chr3L:4353774-4353894 2.59e-02 98_[+1(6.52e-05)]_14 chr3R:22108445-22108565 1.86e-01 120 chr3R:19014946-19015066 1.81e-01 120 chr3R:29581637-29581757 5.82e-01 120 chr2R:20195231-20195351 8.00e-01 120 chr3L:775103-775223 2.49e-01 120 chr2L:7150956-7151076 5.34e-02 120 chr3L:11285278-11285398 9.98e-01 120 chr3L:11291642-11291762 7.51e-01 120 chr3L:10767316-10767436 4.76e-01 120 chr3R:8469848-8469968 8.71e-01 120 chr2R:18994155-18994275 4.37e-01 120 chr2L:13876795-13876915 9.61e-01 120 chr3R:23067524-23067644 9.66e-01 120 chr2R:10160317-10160437 4.08e-01 120 chr3R:16769538-16769658 2.32e-01 120 chr3L:3970524-3970644 3.43e-02 120 chrX:11379261-11379381 3.50e-01 120 chrX:14213627-14213747 4.91e-07 35_[+4(5.43e-07)]_9_[+2(6.89e-06)]_\ 60 chr3L:18272442-18272562 2.80e-01 120 chr3L:18114112-18114232 6.07e-01 120 chrX:10573655-10573775 8.65e-01 120 chr2R:7054352-7054472 6.84e-01 120 chr2R:23578524-23578644 4.64e-02 120 chr2L:17558239-17558359 8.71e-01 120 chr3R:5413061-5413181 9.31e-01 120 chr3R:30164200-30164320 7.84e-01 120 chr2R:11178527-11178647 5.02e-04 36_[+2(1.08e-06)]_76 chr3L:10893529-10893649 8.58e-01 120 chr3R:10648930-10649050 1.87e-04 7_[+3(1.63e-06)]_11_[+4(2.20e-05)]_\ 86 chr3L:3786913-3787033 6.91e-01 120 chr3L:20276750-20276870 5.82e-02 120 chr3L:5952166-5952286 9.82e-01 120 chr3L:10745698-10745818 9.88e-01 120 chrX:13764550-13764670 3.41e-01 120 chr3R:14875709-14875829 2.03e-01 120 chr3R:9344927-9345047 9.29e-01 120 chr2L:9206530-9206650 8.41e-01 120 chr2R:8734645-8734765 2.41e-01 120 chr3R:10449136-10449256 9.18e-01 120 chr3L:11408890-11409010 2.08e-01 120 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (5) found. ******************************************************************************** CPU: c27n07.farnam.hpc.yale.internal ********************************************************************************