******************************************************************************** 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/HLH106.fasta CONTROL SEQUENCES= --none-- ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ chr3R:29506714-29506834 1.0000 120 chr3R:17122912-17123032 1.0000 120 chr3R:15588709-15588829 1.0000 120 chr2R:9065319-9065439 1.0000 120 chr3L:9033685-9033805 1.0000 120 chr3L:21108591-21108711 1.0000 120 chr2L:14400781-14400901 1.0000 120 chr3L:12915584-12915704 1.0000 120 chr2L:4797721-4797841 1.0000 120 chr3R:18895367-18895487 1.0000 120 chr3R:14730260-14730380 1.0000 120 chr3L:5633729-5633849 1.0000 120 chr2L:5393450-5393570 1.0000 120 chr3L:3246957-3247077 1.0000 120 chr3R:17825924-17826044 1.0000 120 chrX:9062789-9062909 1.0000 120 chr3R:23496607-23496727 1.0000 120 chr2L:1668896-1669016 1.0000 120 chr3R:30689760-30689880 1.0000 120 chr2L:15463641-15463761 1.0000 120 chrX:18273273-18273393 1.0000 120 chr3L:16177310-16177430 1.0000 120 chr3L:17613616-17613736 1.0000 120 chr3L:12096868-12096988 1.0000 120 chr3L:8371033-8371153 1.0000 120 chr3R:19603120-19603240 1.0000 120 chr3R:21649639-21649759 1.0000 120 chr3L:602614-602734 1.0000 120 chr2R:24237440-24237560 1.0000 120 chr3R:23148523-23148643 1.0000 120 chrX:2452896-2453016 1.0000 120 chrX:2648095-2648215 1.0000 120 chr3L:16489924-16490044 1.0000 120 chr2L:11326610-11326730 1.0000 120 chrX:14750579-14750699 1.0000 120 chrX:15530530-15530650 1.0000 120 chr2R:22316579-22316699 1.0000 120 chr3L:10411770-10411890 1.0000 120 chr2L:7909347-7909467 1.0000 120 chr3L:6369828-6369948 1.0000 120 chr2L:9981952-9982072 1.0000 120 chr3R:14918353-14918473 1.0000 120 chr3L:11373998-11374118 1.0000 120 chrX:3437660-3437780 1.0000 120 chr2L:10972356-10972476 1.0000 120 chrX:8895073-8895193 1.0000 120 chr2L:18003694-18003814 1.0000 120 chr3L:3423127-3423247 1.0000 120 chr2R:19187320-19187440 1.0000 120 chr2L:12823713-12823833 1.0000 120 chr3L:1389048-1389168 1.0000 120 chr2L:18678355-18678475 1.0000 120 chrX:14118609-14118729 1.0000 120 chr2L:16271131-16271251 1.0000 120 chrX:16930518-16930638 1.0000 120 chrX:13541080-13541200 1.0000 120 chr2R:16685718-16685838 1.0000 120 chr2L:3554059-3554179 1.0000 120 chr3R:29283338-29283458 1.0000 120 chr3L:9742476-9742596 1.0000 120 chr3L:16174913-16175033 1.0000 120 chrX:12507718-12507838 1.0000 120 chrX:8866387-8866507 1.0000 120 chr3L:13212985-13213105 1.0000 120 chrX:6030159-6030279 1.0000 120 chr3R:10670081-10670201 1.0000 120 chr3L:7792348-7792468 1.0000 120 chr2R:15825515-15825635 1.0000 120 chrX:2196188-2196308 1.0000 120 chr3R:29076161-29076281 1.0000 120 chr3R:4243310-4243430 1.0000 120 chr3R:22194891-22195011 1.0000 120 chrX:17551092-17551212 1.0000 120 chr2L:5428864-5428984 1.0000 120 chr3R:20765805-20765925 1.0000 120 chr3L:15762084-15762204 1.0000 120 chr3R:31308967-31309087 1.0000 120 chrX:8491107-8491227 1.0000 120 chr3L:7994070-7994190 1.0000 120 chr2R:24822650-24822770 1.0000 120 chr2L:7419505-7419625 1.0000 120 chr3R:11614626-11614746 1.0000 120 chr3L:2865706-2865826 1.0000 120 chr3L:12016313-12016433 1.0000 120 chr2L:21020161-21020281 1.0000 120 chrX:5026833-5026953 1.0000 120 chr2L:5386373-5386493 1.0000 120 chrX:1320563-1320683 1.0000 120 chrX:18256634-18256754 1.0000 120 chr2L:8855614-8855734 1.0000 120 chr2L:13999085-13999205 1.0000 120 chr3R:29763909-29764029 1.0000 120 chr3R:11154007-11154127 1.0000 120 chr3L:21100560-21100680 1.0000 120 chr3R:14398072-14398192 1.0000 120 chr3L:17506163-17506283 1.0000 120 chr3R:10466445-10466565 1.0000 120 chr3R:27092376-27092496 1.0000 120 chrX:11925365-11925485 1.0000 120 chr2L:17749114-17749234 1.0000 120 chr2R:6147620-6147740 1.0000 120 chr3R:11805700-11805820 1.0000 120 chr3L:15762933-15763053 1.0000 120 chrX:5025447-5025567 1.0000 120 chr3R:26192416-26192536 1.0000 120 chr3R:29279726-29279846 1.0000 120 chr2R:11509666-11509786 1.0000 120 chr2L:7992078-7992198 1.0000 120 chrX:8667857-8667977 1.0000 120 chrX:14074257-14074377 1.0000 120 chr2R:6693144-6693264 1.0000 120 chr3R:8142248-8142368 1.0000 120 chr2R:23237480-23237600 1.0000 120 chr3L:5819458-5819578 1.0000 120 chr3L:5851662-5851782 1.0000 120 chr2L:11052516-11052636 1.0000 120 chrX:10104613-10104733 1.0000 120 chr2R:13935256-13935376 1.0000 120 chr2L:16519724-16519844 1.0000 120 chrX:8730434-8730554 1.0000 120 chr3L:2838340-2838460 1.0000 120 chr2R:6994717-6994837 1.0000 120 chr3L:16015945-16016065 1.0000 120 chr3L:5851862-5851982 1.0000 120 chr2L:18466333-18466453 1.0000 120 chrX:18272535-18272655 1.0000 120 chr2L:3341697-3341817 1.0000 120 chr3L:18030130-18030250 1.0000 120 chr2R:6144384-6144504 1.0000 120 chr2R:16818823-16818943 1.0000 120 chr3R:23191559-23191679 1.0000 120 chr2L:7376301-7376421 1.0000 120 chr4:60423-60543 1.0000 120 chr3R:30256358-30256478 1.0000 120 chrX:17814936-17815056 1.0000 120 chr2L:7574384-7574504 1.0000 120 chr3R:27593320-27593440 1.0000 120 chr3L:8822353-8822473 1.0000 120 chr3L:8368797-8368917 1.0000 120 chr2L:18966974-18967094 1.0000 120 chr3L:6364362-6364482 1.0000 120 chr3L:11467132-11467252 1.0000 120 chr2L:17421487-17421607 1.0000 120 chr3L:13994482-13994602 1.0000 120 chr2R:10237822-10237942 1.0000 120 chr2L:7104729-7104849 1.0000 120 chr2R:22529777-22529897 1.0000 120 chr2L:20956892-20957012 1.0000 120 chr2R:19913859-19913979 1.0000 120 chr2L:11328483-11328603 1.0000 120 chr2R:21313127-21313247 1.0000 120 chr2R:12951424-12951544 1.0000 120 chr3R:29538571-29538691 1.0000 120 chr2R:24629566-24629686 1.0000 120 chr2L:18003150-18003270 1.0000 120 chr2L:15385473-15385593 1.0000 120 chr3R:25634001-25634121 1.0000 120 chr2R:6556948-6557068 1.0000 120 chr2L:7323110-7323230 1.0000 120 chr3L:8157156-8157276 1.0000 120 chr3R:8154097-8154217 1.0000 120 chr2R:15842719-15842839 1.0000 120 chr3R:8029711-8029831 1.0000 120 chr3L:10697076-10697196 1.0000 120 chr3L:1458181-1458301 1.0000 120 chr2L:10616011-10616131 1.0000 120 chr3R:27171250-27171370 1.0000 120 chr2L:11306229-11306349 1.0000 120 chr2R:14009454-14009574 1.0000 120 chr2R:6219996-6220116 1.0000 120 chr3L:728022-728142 1.0000 120 chr3L:14611513-14611633 1.0000 120 chr2L:21847410-21847530 1.0000 120 chr3L:664017-664137 1.0000 120 chr3L:2830107-2830227 1.0000 120 chr2L:6022927-6023047 1.0000 120 chr3L:14610596-14610716 1.0000 120 chrX:6642982-6643102 1.0000 120 chr3R:6397843-6397963 1.0000 120 chrX:7491066-7491186 1.0000 120 chr3R:26859353-26859473 1.0000 120 chr2L:4211379-4211499 1.0000 120 chrX:6542428-6542548 1.0000 120 chrX:13312316-13312436 1.0000 120 chr3L:6285568-6285688 1.0000 120 chrX:5026175-5026295 1.0000 120 chr3L:16183213-16183333 1.0000 120 chr3R:23888774-23888894 1.0000 120 chr3L:512000-512120 1.0000 120 chr3R:5100467-5100587 1.0000 120 chr3L:2835138-2835258 1.0000 120 chr3R:8858105-8858225 1.0000 120 chr2R:23894903-23895023 1.0000 120 chr3L:7783512-7783632 1.0000 120 chr3R:13793458-13793578 1.0000 120 chr3R:22175854-22175974 1.0000 120 chrX:9892983-9893103 1.0000 120 chr3R:10579673-10579793 1.0000 120 chr3L:12616580-12616700 1.0000 120 chr2L:20204744-20204864 1.0000 120 chrX:3381147-3381267 1.0000 120 chr2R:12013419-12013539 1.0000 120 chrX:18834552-18834672 1.0000 120 chr3R:11872832-11872952 1.0000 120 chr3R:18742417-18742537 1.0000 120 chrX:17490009-17490129 1.0000 120 chr3L:1683260-1683380 1.0000 120 chr3L:1374581-1374701 1.0000 120 chr3R:30281398-30281518 1.0000 120 chr3L:15977687-15977807 1.0000 120 chrX:6624490-6624610 1.0000 120 chr3R:15566498-15566618 1.0000 120 chr3R:15213726-15213846 1.0000 120 chr3L:14055359-14055479 1.0000 120 chr2L:382938-383058 1.0000 120 chr3L:1388239-1388359 1.0000 120 chr3R:14048941-14049061 1.0000 120 chrX:3346696-3346816 1.0000 120 chr3L:19557341-19557461 1.0000 120 chr2L:5501452-5501572 1.0000 120 chr2R:9674755-9674875 1.0000 120 chr3R:13372070-13372190 1.0000 120 chr2R:17836059-17836179 1.0000 120 chr2R:9711963-9712083 1.0000 120 chrX:15642167-15642287 1.0000 120 chr2R:18894880-18895000 1.0000 120 chr3L:11298464-11298584 1.0000 120 chrX:7534976-7535096 1.0000 120 chr2L:5493075-5493195 1.0000 120 chr3R:12443325-12443445 1.0000 120 chr3L:761864-761984 1.0000 120 chr2L:16406677-16406797 1.0000 120 chr3R:30811348-30811468 1.0000 120 chr3L:2879914-2880034 1.0000 120 chr3R:13941555-13941675 1.0000 120 chr3L:20952186-20952306 1.0000 120 chrX:7968440-7968560 1.0000 120 chr3R:4873865-4873985 1.0000 120 chr3L:3395485-3395605 1.0000 120 chr3L:5863056-5863176 1.0000 120 chr3R:26235178-26235298 1.0000 120 chr3R:27201690-27201810 1.0000 120 chr3L:19046493-19046613 1.0000 120 chr2R:19935599-19935719 1.0000 120 chr3R:18914099-18914219 1.0000 120 chrX:12760792-12760912 1.0000 120 chr3R:13849462-13849582 1.0000 120 chr2R:18209808-18209928 1.0000 120 chrX:12663046-12663166 1.0000 120 chrX:8145652-8145772 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_HLH106/ -dna -nmotifs 5 -w 8 -maxsize 250000 -nostatus ../result/final_prediction/fly/fasta/RankLinear8.0_60/HLH106.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 0.36 C 0.142 G 0.138 T 0.36 Background letter frequencies (from file dataset with add-one prior applied): A 0.36 C 0.142 G 0.138 T 0.36 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF GGCGGCGC MEME-1 width = 8 sites = 7 llr = 85 E-value = 1.4e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif GGCGGCGC MEME-1 Description -------------------------------------------------------------------------------- Simplified A ::::::1: pos.-specific C 3:9:39:a probability G 77:a719: matrix T :31::::: bits 2.9 * * 2.6 * * 2.3 * * * 2.0 * ****** Relative 1.7 ******** Entropy 1.4 ******** (17.6 bits) 1.1 ******** 0.9 ******** 0.6 ******** 0.3 ******** 0.0 -------- Multilevel GGCGGCGC consensus CT C sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGCGGCGC MEME-1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chrX:6030159-6030279 23 1.43e-07 AATCGAATAA GGCGGCGC GTCAATGATG chr3L:5851662-5851782 9 4.38e-07 ATGACAGA CGCGGCGC AAGATGCAAA chrX:18256634-18256754 107 1.10e-06 ACATTCAGCA GTCGGCGC GTCAGC chrX:12760792-12760912 14 2.13e-06 ATGAACACCG CGCGGGGC AACTTATGta chr3R:23148523-23148643 75 2.13e-06 CCATGATGAT GGTGGCGC GGGTCGGAGG chr3L:9033685-9033805 85 2.90e-06 ACTAACAAAA GTCGCCGC ACTTTCATAG chr2R:21313127-21313247 57 4.92e-06 TTCTCACGTA GGCGCCAC ATGTCAATAG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGCGGCGC MEME-1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrX:6030159-6030279 1.4e-07 22_[+1]_90 chr3L:5851662-5851782 4.4e-07 8_[+1]_104 chrX:18256634-18256754 1.1e-06 106_[+1]_6 chrX:12760792-12760912 2.1e-06 13_[+1]_99 chr3R:23148523-23148643 2.1e-06 74_[+1]_38 chr3L:9033685-9033805 2.9e-06 84_[+1]_28 chr2R:21313127-21313247 4.9e-06 56_[+1]_56 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGCGGCGC MEME-1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF GGCGGCGC width=8 seqs=7 chrX:6030159-6030279 ( 23) GGCGGCGC 1 chr3L:5851662-5851782 ( 9) CGCGGCGC 1 chrX:18256634-18256754 ( 107) GTCGGCGC 1 chrX:12760792-12760912 ( 14) CGCGGGGC 1 chr3R:23148523-23148643 ( 75) GGTGGCGC 1 chr3L:9033685-9033805 ( 85) GTCGCCGC 1 chr2R:21313127-21313247 ( 57) GGCGCCAC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGCGGCGC MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 28250 bayes= 12.5841 E= 1.4e+001 -945 101 237 -945 -945 -945 237 -33 -945 260 -945 -133 -945 -945 285 -945 -945 101 237 -945 -945 260 5 -945 -133 -945 263 -945 -945 282 -945 -945 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGCGGCGC MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 7 E= 1.4e+001 0.000000 0.285714 0.714286 0.000000 0.000000 0.000000 0.714286 0.285714 0.000000 0.857143 0.000000 0.142857 0.000000 0.000000 1.000000 0.000000 0.000000 0.285714 0.714286 0.000000 0.000000 0.857143 0.142857 0.000000 0.142857 0.000000 0.857143 0.000000 0.000000 1.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGCGGCGC MEME-1 regular expression -------------------------------------------------------------------------------- [GC][GT]CG[GC]CGC -------------------------------------------------------------------------------- Time 7.51 secs. ******************************************************************************** ******************************************************************************** MOTIF GCCGSACC MEME-2 width = 8 sites = 3 llr = 41 E-value = 2.9e+003 ******************************************************************************** -------------------------------------------------------------------------------- Motif GCCGSACC MEME-2 Description -------------------------------------------------------------------------------- Simplified A :::::7:: pos.-specific C :aa:3:aa probability G a::a73:: matrix T :::::::: bits 2.9 **** ** 2.6 **** ** 2.3 **** ** 2.0 ***** ** Relative 1.7 ***** ** Entropy 1.4 ***** ** (19.9 bits) 1.1 ******** 0.9 ******** 0.6 ******** 0.3 ******** 0.0 -------- Multilevel GCCGGACC consensus CG sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCCGSACC MEME-2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr3L:6285568-6285688 65 1.47e-07 TTACCAAATT GCCGGGCC AATTCGCCCG chr3L:1683260-1683380 111 5.32e-07 ACGCCCCTGT GCCGGACC CC chr3R:20765805-20765925 46 1.08e-06 CTCGAAACAC GCCGCACC TCTCGCTTTA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCCGSACC MEME-2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr3L:6285568-6285688 1.5e-07 64_[+2]_48 chr3L:1683260-1683380 5.3e-07 110_[+2]_2 chr3R:20765805-20765925 1.1e-06 45_[+2]_67 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCCGSACC MEME-2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF GCCGSACC width=8 seqs=3 chr3L:6285568-6285688 ( 65) GCCGGGCC 1 chr3L:1683260-1683380 ( 111) GCCGGACC 1 chr3R:20765805-20765925 ( 46) GCCGCACC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCCGSACC MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 28250 bayes= 13.6483 E= 2.9e+003 -823 -823 285 -823 -823 282 -823 -823 -823 282 -823 -823 -823 -823 285 -823 -823 123 227 -823 89 -823 127 -823 -823 282 -823 -823 -823 282 -823 -823 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCCGSACC MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 3 E= 2.9e+003 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 1.000000 0.000000 0.000000 0.333333 0.666667 0.000000 0.666667 0.000000 0.333333 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCCGSACC MEME-2 regular expression -------------------------------------------------------------------------------- GCCG[GC][AG]CC -------------------------------------------------------------------------------- Time 13.89 secs. ******************************************************************************** ******************************************************************************** MOTIF TGGGGAGG MEME-3 width = 8 sites = 2 llr = 28 E-value = 5.5e+003 ******************************************************************************** -------------------------------------------------------------------------------- Motif TGGGGAGG MEME-3 Description -------------------------------------------------------------------------------- Simplified A :::::a:: pos.-specific C :::::::: probability G :aaaa:aa matrix T a::::::: bits 2.9 **** ** 2.6 **** ** 2.3 **** ** 2.0 **** ** Relative 1.7 **** ** Entropy 1.4 ******** (20.1 bits) 1.1 ******** 0.9 ******** 0.6 ******** 0.3 ******** 0.0 -------- Multilevel TGGGGAGG consensus sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TGGGGAGG MEME-3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr3R:10466445-10466565 49 8.95e-07 TTAACCAATA TGGGGAGG TATTTTTTTA chr3R:29506714-29506834 79 8.95e-07 ACTACATTTA TGGGGAGG CATATAAAAT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TGGGGAGG MEME-3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr3R:10466445-10466565 9e-07 48_[+3]_64 chr3R:29506714-29506834 9e-07 78_[+3]_34 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TGGGGAGG MEME-3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF TGGGGAGG width=8 seqs=2 chr3R:10466445-10466565 ( 49) TGGGGAGG 1 chr3R:29506714-29506834 ( 79) TGGGGAGG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TGGGGAGG MEME-3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 28250 bayes= 13.7859 E= 5.5e+003 -765 -765 -765 147 -765 -765 285 -765 -765 -765 285 -765 -765 -765 285 -765 -765 -765 285 -765 147 -765 -765 -765 -765 -765 285 -765 -765 -765 285 -765 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TGGGGAGG MEME-3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 2 E= 5.5e+003 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 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 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TGGGGAGG MEME-3 regular expression -------------------------------------------------------------------------------- TGGGGAGG -------------------------------------------------------------------------------- Time 20.18 secs. ******************************************************************************** ******************************************************************************** MOTIF CSCCSTGC MEME-4 width = 8 sites = 3 llr = 40 E-value = 7.4e+003 ******************************************************************************** -------------------------------------------------------------------------------- Motif CSCCSTGC MEME-4 Description -------------------------------------------------------------------------------- Simplified A :::::::: pos.-specific C a7aa7::a probability G :3::3:a: matrix T :::::a:: bits 2.9 * ** ** 2.6 * ** ** 2.3 * ** ** 2.0 ***** ** Relative 1.7 ***** ** Entropy 1.4 ******** (19.4 bits) 1.1 ******** 0.9 ******** 0.6 ******** 0.3 ******** 0.0 -------- Multilevel CCCCCTGC consensus G G sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CSCCSTGC MEME-4 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr3R:20765805-20765925 112 4.07e-07 GGCCTCCACC CCCCCTGC A chr2L:15385473-15385593 105 1.20e-06 ATAATATAAA CGCCCTGC ATCTAGAT chr3R:23148523-23148643 22 1.20e-06 CAGATCTCCT CCCCGTGC TGCCCTTGTA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CSCCSTGC MEME-4 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr3R:20765805-20765925 4.1e-07 111_[+4]_1 chr2L:15385473-15385593 1.2e-06 104_[+4]_8 chr3R:23148523-23148643 1.2e-06 21_[+4]_91 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CSCCSTGC MEME-4 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF CSCCSTGC width=8 seqs=3 chr3R:20765805-20765925 ( 112) CCCCCTGC 1 chr2L:15385473-15385593 ( 105) CGCCCTGC 1 chr3R:23148523-23148643 ( 22) CCCCGTGC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CSCCSTGC MEME-4 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 28250 bayes= 12.8598 E= 7.4e+003 -823 282 -823 -823 -823 223 127 -823 -823 282 -823 -823 -823 282 -823 -823 -823 223 127 -823 -823 -823 -823 147 -823 -823 285 -823 -823 282 -823 -823 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CSCCSTGC MEME-4 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 3 E= 7.4e+003 0.000000 1.000000 0.000000 0.000000 0.000000 0.666667 0.333333 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.666667 0.333333 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 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CSCCSTGC MEME-4 regular expression -------------------------------------------------------------------------------- C[CG]CC[CG]TGC -------------------------------------------------------------------------------- Time 26.47 secs. ******************************************************************************** ******************************************************************************** MOTIF GCAGYSGC MEME-5 width = 8 sites = 3 llr = 40 E-value = 1.6e+004 ******************************************************************************** -------------------------------------------------------------------------------- Motif GCAGYSGC MEME-5 Description -------------------------------------------------------------------------------- Simplified A ::a::::: pos.-specific C :a::73:a probability G a::a:7a: matrix T ::::3::: bits 2.9 ** * ** 2.6 ** * ** 2.3 ** * ** 2.0 ** * *** Relative 1.7 ** * *** Entropy 1.4 ******** (19.1 bits) 1.1 ******** 0.9 ******** 0.6 ******** 0.3 ******** 0.0 -------- Multilevel GCAGCGGC consensus TC sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCAGYSGC MEME-5 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chrX:13541080-13541200 80 3.74e-07 TTCTCGCTGT GCAGCGGC AACACTACCA chrX:8667857-8667977 34 7.59e-07 ATTTATGCTT GCAGCCGC ATAACAATCT chr3R:18895367-18895487 96 1.71e-06 TACATTCATA GCAGTGGC ATTCGCACAC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCAGYSGC MEME-5 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrX:13541080-13541200 3.7e-07 79_[+5]_33 chrX:8667857-8667977 7.6e-07 33_[+5]_79 chr3R:18895367-18895487 1.7e-06 95_[+5]_17 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCAGYSGC MEME-5 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF GCAGYSGC width=8 seqs=3 chrX:13541080-13541200 ( 80) GCAGCGGC 1 chrX:8667857-8667977 ( 34) GCAGCCGC 1 chr3R:18895367-18895487 ( 96) GCAGTGGC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCAGYSGC MEME-5 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 28250 bayes= 13.6483 E= 1.6e+004 -823 -823 285 -823 -823 282 -823 -823 147 -823 -823 -823 -823 -823 285 -823 -823 223 -823 -11 -823 123 227 -823 -823 -823 285 -823 -823 282 -823 -823 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCAGYSGC MEME-5 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 3 E= 1.6e+004 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 0.666667 0.000000 0.333333 0.000000 0.333333 0.666667 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCAGYSGC MEME-5 regular expression -------------------------------------------------------------------------------- GCAG[CT][GC]GC -------------------------------------------------------------------------------- Time 32.70 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr3R:29506714-29506834 1.75e-03 78_[+3(8.95e-07)]_34 chr3R:17122912-17123032 9.73e-01 120 chr3R:15588709-15588829 9.99e-01 120 chr2R:9065319-9065439 6.93e-02 120 chr3L:9033685-9033805 2.25e-05 84_[+1(2.90e-06)]_28 chr3L:21108591-21108711 1.00e+00 120 chr2L:14400781-14400901 8.17e-01 120 chr3L:12915584-12915704 5.99e-01 120 chr2L:4797721-4797841 5.54e-01 120 chr3R:18895367-18895487 7.64e-03 95_[+5(1.71e-06)]_17 chr3R:14730260-14730380 9.37e-01 120 chr3L:5633729-5633849 6.36e-01 120 chr2L:5393450-5393570 9.96e-01 120 chr3L:3246957-3247077 9.59e-01 120 chr3R:17825924-17826044 9.74e-01 120 chrX:9062789-9062909 5.82e-01 120 chr3R:23496607-23496727 7.31e-01 120 chr2L:1668896-1669016 1.86e-01 120 chr3R:30689760-30689880 9.42e-01 120 chr2L:15463641-15463761 8.61e-01 120 chrX:18273273-18273393 9.45e-01 120 chr3L:16177310-16177430 9.75e-01 120 chr3L:17613616-17613736 7.44e-01 120 chr3L:12096868-12096988 1.00e+00 120 chr3L:8371033-8371153 6.86e-01 120 chr3R:19603120-19603240 2.87e-02 68_[+1(1.63e-05)]_44 chr3R:21649639-21649759 9.98e-01 120 chr3L:602614-602734 1.48e-03 70_[+4(6.81e-05)]_42 chr2R:24237440-24237560 9.74e-01 120 chr3R:23148523-23148643 2.39e-07 21_[+4(1.20e-06)]_28_[+1(2.08e-05)]_\ 9_[+1(2.13e-06)]_38 chrX:2452896-2453016 3.91e-02 120 chrX:2648095-2648215 1.24e-04 29_[+4(6.81e-05)]_[+5(6.96e-05)]_75 chr3L:16489924-16490044 9.44e-01 120 chr2L:11326610-11326730 1.30e-01 120 chrX:14750579-14750699 9.93e-01 120 chrX:15530530-15530650 1.00e+00 120 chr2R:22316579-22316699 7.39e-01 120 chr3L:10411770-10411890 8.95e-01 120 chr2L:7909347-7909467 9.99e-01 120 chr3L:6369828-6369948 9.93e-01 120 chr2L:9981952-9982072 9.61e-01 120 chr3R:14918353-14918473 7.58e-01 120 chr3L:11373998-11374118 1.00e+00 120 chrX:3437660-3437780 2.03e-01 120 chr2L:10972356-10972476 7.04e-01 120 chrX:8895073-8895193 4.60e-01 120 chr2L:18003694-18003814 4.70e-02 120 chr3L:3423127-3423247 5.83e-01 120 chr2R:19187320-19187440 9.97e-01 120 chr2L:12823713-12823833 9.46e-01 120 chr3L:1389048-1389168 5.60e-03 120 chr2L:18678355-18678475 6.17e-01 120 chrX:14118609-14118729 6.60e-02 90_[+1(5.42e-05)]_22 chr2L:16271131-16271251 9.81e-01 120 chrX:16930518-16930638 9.11e-01 120 chrX:13541080-13541200 4.77e-06 79_[+5(3.74e-07)]_33 chr2R:16685718-16685838 1.61e-01 120 chr2L:3554059-3554179 6.20e-01 120 chr3R:29283338-29283458 1.53e-01 120 chr3L:9742476-9742596 5.74e-01 120 chr3L:16174913-16175033 8.80e-01 120 chrX:12507718-12507838 5.95e-01 120 chrX:8866387-8866507 1.00e+00 120 chr3L:13212985-13213105 2.01e-01 120 chrX:6030159-6030279 2.00e-05 22_[+1(1.43e-07)]_90 chr3R:10670081-10670201 9.91e-01 120 chr3L:7792348-7792468 3.62e-02 120 chr2R:15825515-15825635 9.79e-01 120 chrX:2196188-2196308 2.12e-01 120 chr3R:29076161-29076281 4.59e-01 120 chr3R:4243310-4243430 9.01e-01 120 chr3R:22194891-22195011 6.82e-01 120 chrX:17551092-17551212 9.64e-01 120 chr2L:5428864-5428984 9.95e-01 120 chr3R:20765805-20765925 1.22e-07 45_[+2(1.08e-06)]_58_[+4(4.07e-07)]_\ 1 chr3L:15762084-15762204 3.31e-01 120 chr3R:31308967-31309087 1.69e-02 85_[+5(6.96e-05)]_27 chrX:8491107-8491227 8.45e-01 120 chr3L:7994070-7994190 9.34e-01 120 chr2R:24822650-24822770 8.37e-01 120 chr2L:7419505-7419625 1.21e-01 120 chr3R:11614626-11614746 2.92e-02 120 chr3L:2865706-2865826 6.69e-01 120 chr3L:12016313-12016433 4.55e-01 120 chr2L:21020161-21020281 8.52e-01 120 chrX:5026833-5026953 9.99e-01 120 chr2L:5386373-5386493 3.20e-01 120 chrX:1320563-1320683 5.50e-01 120 chrX:18256634-18256754 6.21e-05 106_[+1(1.10e-06)]_6 chr2L:8855614-8855734 2.85e-01 120 chr2L:13999085-13999205 1.00e+00 120 chr3R:29763909-29764029 8.57e-01 120 chr3R:11154007-11154127 9.50e-01 120 chr3L:21100560-21100680 4.15e-01 120 chr3R:14398072-14398192 8.20e-01 120 chr3L:17506163-17506283 7.74e-01 120 chr3R:10466445-10466565 3.71e-02 48_[+3(8.95e-07)]_64 chr3R:27092376-27092496 4.80e-02 120 chrX:11925365-11925485 9.52e-01 120 chr2L:17749114-17749234 2.54e-01 120 chr2R:6147620-6147740 9.67e-01 120 chr3R:11805700-11805820 2.39e-01 120 chr3L:15762933-15763053 3.32e-01 120 chrX:5025447-5025567 8.40e-01 120 chr3R:26192416-26192536 6.56e-01 120 chr3R:29279726-29279846 2.82e-01 120 chr2R:11509666-11509786 6.01e-01 120 chr2L:7992078-7992198 2.81e-01 120 chrX:8667857-8667977 3.48e-04 33_[+5(7.59e-07)]_79 chrX:14074257-14074377 3.94e-01 120 chr2R:6693144-6693264 9.75e-01 120 chr3R:8142248-8142368 5.95e-01 120 chr2R:23237480-23237600 6.85e-03 9_[+3(3.76e-05)]_103 chr3L:5819458-5819578 4.40e-01 120 chr3L:5851662-5851782 7.22e-06 8_[+1(4.38e-07)]_104 chr2L:11052516-11052636 2.11e-01 120 chrX:10104613-10104733 3.51e-01 120 chr2R:13935256-13935376 7.45e-01 120 chr2L:16519724-16519844 4.86e-01 120 chrX:8730434-8730554 5.33e-02 [+3(3.76e-05)]_112 chr3L:2838340-2838460 5.98e-01 120 chr2R:6994717-6994837 4.60e-01 120 chr3L:16015945-16016065 5.18e-01 120 chr3L:5851862-5851982 2.54e-01 120 chr2L:18466333-18466453 5.10e-02 120 chrX:18272535-18272655 5.56e-01 120 chr2L:3341697-3341817 2.00e-01 91_[+1(5.42e-05)]_21 chr3L:18030130-18030250 9.97e-01 120 chr2R:6144384-6144504 2.37e-01 120 chr2R:16818823-16818943 9.75e-01 120 chr3R:23191559-23191679 9.63e-01 120 chr2L:7376301-7376421 3.93e-01 120 chr4:60423-60543 1.00e+00 120 chr3R:30256358-30256478 8.77e-01 120 chrX:17814936-17815056 8.54e-01 120 chr2L:7574384-7574504 9.26e-01 120 chr3R:27593320-27593440 9.78e-01 120 chr3L:8822353-8822473 2.22e-01 120 chr3L:8368797-8368917 1.02e-01 120 chr2L:18966974-18967094 1.00e+00 120 chr3L:6364362-6364482 9.95e-01 120 chr3L:11467132-11467252 4.82e-01 120 chr2L:17421487-17421607 1.77e-01 120 chr3L:13994482-13994602 9.55e-01 120 chr2R:10237822-10237942 6.33e-01 120 chr2L:7104729-7104849 7.91e-01 120 chr2R:22529777-22529897 3.13e-02 93_[+4(2.02e-05)]_19 chr2L:20956892-20957012 5.04e-01 120 chr2R:19913859-19913979 6.82e-01 120 chr2L:11328483-11328603 4.83e-01 120 chr2R:21313127-21313247 4.58e-04 56_[+1(4.92e-06)]_56 chr2R:12951424-12951544 8.50e-01 120 chr3R:29538571-29538691 8.50e-01 120 chr2R:24629566-24629686 7.68e-03 120 chr2L:18003150-18003270 8.48e-01 120 chr2L:15385473-15385593 4.62e-03 104_[+4(1.20e-06)]_8 chr3R:25634001-25634121 9.38e-01 120 chr2R:6556948-6557068 1.49e-01 120 chr2L:7323110-7323230 9.52e-01 120 chr3L:8157156-8157276 2.51e-01 120 chr3R:8154097-8154217 9.53e-01 120 chr2R:15842719-15842839 9.82e-01 120 chr3R:8029711-8029831 1.00e+00 120 chr3L:10697076-10697196 9.96e-01 120 chr3L:1458181-1458301 7.34e-01 120 chr2L:10616011-10616131 8.28e-01 120 chr3R:27171250-27171370 9.50e-01 120 chr2L:11306229-11306349 2.82e-01 120 chr2R:14009454-14009574 6.35e-01 120 chr2R:6219996-6220116 4.10e-01 120 chr3L:728022-728142 7.60e-03 64_[+4(2.42e-05)]_48 chr3L:14611513-14611633 1.00e+00 120 chr2L:21847410-21847530 1.68e-02 120 chr3L:664017-664137 9.01e-02 120 chr3L:2830107-2830227 3.40e-01 120 chr2L:6022927-6023047 6.87e-01 120 chr3L:14610596-14610716 5.46e-01 120 chrX:6642982-6643102 8.63e-01 120 chr3R:6397843-6397963 2.18e-01 120 chrX:7491066-7491186 1.14e-01 120 chr3R:26859353-26859473 3.83e-01 120 chr2L:4211379-4211499 9.18e-01 120 chrX:6542428-6542548 7.64e-01 120 chrX:13312316-13312436 5.86e-01 120 chr3L:6285568-6285688 4.42e-05 64_[+2(1.47e-07)]_48 chrX:5026175-5026295 9.67e-01 120 chr3L:16183213-16183333 1.00e+00 120 chr3R:23888774-23888894 6.52e-01 120 chr3L:512000-512120 5.79e-02 120 chr3R:5100467-5100587 9.10e-01 120 chr3L:2835138-2835258 5.99e-02 99_[+5(3.87e-05)]_13 chr3R:8858105-8858225 7.57e-01 120 chr2R:23894903-23895023 5.72e-01 120 chr3L:7783512-7783632 3.16e-01 120 chr3R:13793458-13793578 9.91e-01 120 chr3R:22175854-22175974 4.84e-01 120 chrX:9892983-9893103 3.82e-01 120 chr3R:10579673-10579793 4.19e-01 120 chr3L:12616580-12616700 9.76e-01 120 chr2L:20204744-20204864 8.97e-01 120 chrX:3381147-3381267 4.21e-01 120 chr2R:12013419-12013539 1.21e-01 120 chrX:18834552-18834672 2.61e-01 47_[+5(6.96e-05)]_65 chr3R:11872832-11872952 7.18e-01 120 chr3R:18742417-18742537 9.68e-01 120 chrX:17490009-17490129 9.30e-01 120 chr3L:1683260-1683380 5.52e-06 110_[+2(5.32e-07)]_2 chr3L:1374581-1374701 9.20e-01 120 chr3R:30281398-30281518 1.16e-01 74_[+2(4.73e-05)]_38 chr3L:15977687-15977807 7.57e-01 120 chrX:6624490-6624610 8.26e-01 120 chr3R:15566498-15566618 1.39e-02 120 chr3R:15213726-15213846 9.20e-01 120 chr3L:14055359-14055479 3.12e-01 120 chr2L:382938-383058 9.93e-01 120 chr3L:1388239-1388359 5.30e-03 120 chr3R:14048941-14049061 7.47e-01 120 chrX:3346696-3346816 6.62e-01 120 chr3L:19557341-19557461 9.35e-01 120 chr2L:5501452-5501572 8.52e-02 120 chr2R:9674755-9674875 6.50e-02 88_[+1(7.28e-05)]_24 chr3R:13372070-13372190 9.38e-01 120 chr2R:17836059-17836179 9.48e-01 120 chr2R:9711963-9712083 9.04e-01 120 chrX:15642167-15642287 9.97e-01 120 chr2R:18894880-18895000 9.97e-01 120 chr3L:11298464-11298584 9.92e-01 120 chrX:7534976-7535096 1.00e+00 120 chr2L:5493075-5493195 1.65e-01 120 chr3R:12443325-12443445 1.00e+00 120 chr3L:761864-761984 6.49e-01 120 chr2L:16406677-16406797 3.93e-01 120 chr3R:30811348-30811468 1.22e-01 120 chr3L:2879914-2880034 1.45e-02 87_[+5(9.97e-05)]_25 chr3R:13941555-13941675 1.29e-01 120 chr3L:20952186-20952306 6.17e-01 120 chrX:7968440-7968560 4.80e-01 120 chr3R:4873865-4873985 3.78e-01 120 chr3L:3395485-3395605 1.61e-03 77_[+4(4.90e-05)]_35 chr3L:5863056-5863176 7.05e-01 120 chr3R:26235178-26235298 2.50e-01 120 chr3R:27201690-27201810 4.32e-01 120 chr3L:19046493-19046613 9.94e-01 120 chr2R:19935599-19935719 3.15e-01 120 chr3R:18914099-18914219 1.17e-02 120 chrX:12760792-12760912 1.67e-04 13_[+1(2.13e-06)]_99 chr3R:13849462-13849582 8.99e-01 120 chr2R:18209808-18209928 5.36e-02 29_[+4(4.90e-05)]_83 chrX:12663046-12663166 9.76e-01 120 chrX:8145652-8145772 9.86e-01 120 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (5) found. ******************************************************************************** CPU: c27n08.farnam.hpc.yale.internal ********************************************************************************